Starting phenix.real_space_refine on Sun May 11 12:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxb_29530/05_2025/8fxb_29530.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 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 42 5.16 5 C 5041 2.51 5 N 1318 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7912 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 769 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4789 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 Chain: "E" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1296 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain breaks: 2 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.87, per 1000 atoms: 0.62 Number of scatterers: 7912 At special positions: 0 Unit cell: (85, 100, 130, 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 42 16.00 O 1511 8.00 N 1318 7.00 C 5041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.01 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.01 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-6 " NAG B 1 " - " FUC B 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 90 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 322 " " NAG A 705 " - " ASN A 103 " " NAG B 1 " - " ASN E 343 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 44.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.044A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.557A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.581A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.537A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.784A pdb=" N SER A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.846A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 221 through 249 Proline residue: A 235 - end of helix 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 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.783A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 402 through 413 removed outlier: 5.135A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.029A 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 447 removed outlier: 3.621A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.769A 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 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 515 through 533 removed outlier: 4.197A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.736A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.558A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.724A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.724A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.735A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'E' and resid 451 through 453 removed outlier: 4.774A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 473 through 474 368 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1626 1.33 - 1.45: 2152 1.45 - 1.58: 4277 1.58 - 1.71: 1 1.71 - 1.83: 66 Bond restraints: 8122 Sorted by residual: bond pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 1.457 1.489 -0.033 6.40e-03 2.44e+04 2.64e+01 bond pdb=" N GLN E 493 " pdb=" CA GLN E 493 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.31e-02 5.83e+03 9.39e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.589 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N PHE E 456 " pdb=" CA PHE E 456 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 7.98e+00 ... (remaining 8117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 10553 2.52 - 5.04: 390 5.04 - 7.56: 79 7.56 - 10.08: 4 10.08 - 12.60: 1 Bond angle restraints: 11027 Sorted by residual: angle pdb=" C TYR E 449 " pdb=" CA TYR E 449 " pdb=" CB TYR E 449 " ideal model delta sigma weight residual 111.88 99.28 12.60 1.41e+00 5.03e-01 7.99e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.52 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" C SER A 257 " pdb=" N PRO A 258 " pdb=" CA PRO A 258 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.02e+00 9.61e-01 5.62e+01 angle pdb=" C ARG E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.56 126.96 -7.40 1.01e+00 9.80e-01 5.37e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.89 127.20 -7.31 1.02e+00 9.61e-01 5.14e+01 ... (remaining 11022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 4497 12.97 - 25.94: 243 25.94 - 38.91: 70 38.91 - 51.88: 28 51.88 - 64.85: 23 Dihedral angle restraints: 4861 sinusoidal: 2028 harmonic: 2833 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 93.00 60.95 32.05 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 61.16 31.84 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" C TYR E 449 " pdb=" N TYR E 449 " pdb=" CA TYR E 449 " pdb=" CB TYR E 449 " ideal model delta harmonic sigma weight residual -122.60 -113.36 -9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 828 0.067 - 0.134: 266 0.134 - 0.200: 73 0.200 - 0.267: 11 0.267 - 0.334: 6 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1 FUC B 2 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 2 " pdb=" O5 FUC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.07e+01 chirality pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" C3 NAG A 703 " pdb=" N2 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1181 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.096 2.00e-02 2.50e+03 7.89e-02 7.78e+01 pdb=" C7 NAG A 704 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.125 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG A 705 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 320 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C LEU A 320 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 320 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 321 " 0.016 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 25 2.60 - 3.17: 6708 3.17 - 3.75: 11708 3.75 - 4.32: 17687 4.32 - 4.90: 28333 Nonbonded interactions: 64461 Sorted by model distance: nonbonded pdb=" O ASP A 471 " pdb=" OE2 GLU A 495 " model vdw 2.024 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.271 3.120 nonbonded pdb=" CB LYS L 40 " pdb=" OE1 GLN L 43 " model vdw 2.308 3.440 nonbonded pdb=" O GLU A 495 " pdb=" N TYR A 497 " model vdw 2.340 3.120 nonbonded pdb=" O TYR E 449 " pdb=" CB TYR E 449 " model vdw 2.440 2.752 ... (remaining 64456 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.011 0.062 8137 Z= 0.641 Angle : 1.241 15.581 11064 Z= 0.847 Chirality : 0.073 0.334 1184 Planarity : 0.005 0.079 1410 Dihedral : 10.518 64.853 3025 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.22 % Favored : 96.36 % Rotamer: Outliers : 0.59 % Allowed : 2.02 % Favored : 97.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 962 helix: -0.84 (0.24), residues: 382 sheet: 0.63 (0.39), residues: 146 loop : -0.13 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 117 HIS 0.004 0.001 HIS A 378 PHE 0.021 0.003 PHE L 98 TYR 0.031 0.004 TYR E 495 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.04037 ( 6) link_NAG-ASN : angle 5.65421 ( 18) hydrogen bonds : bond 0.20275 ( 353) hydrogen bonds : angle 7.09615 ( 975) link_BETA1-6 : bond 0.04865 ( 1) link_BETA1-6 : angle 2.96652 ( 3) SS BOND : bond 0.02926 ( 8) SS BOND : angle 4.41897 ( 16) covalent geometry : bond 0.01119 ( 8122) covalent geometry : angle 1.20953 (11027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.860 Fit side-chains REVERT: A 401 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8592 (t-90) outliers start: 5 outliers final: 3 residues processed: 175 average time/residue: 0.1691 time to fit residues: 41.5356 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 55 ASN A 33 ASN A 96 GLN A 535 HIS A 586 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.185725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161541 restraints weight = 9635.676| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.03 r_work: 0.3830 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8137 Z= 0.140 Angle : 0.571 7.809 11064 Z= 0.301 Chirality : 0.042 0.170 1184 Planarity : 0.005 0.064 1410 Dihedral : 5.155 57.474 1212 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.95 % Allowed : 7.59 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 962 helix: 0.51 (0.27), residues: 382 sheet: 0.66 (0.40), residues: 149 loop : 0.14 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 275 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 6) link_NAG-ASN : angle 1.66794 ( 18) hydrogen bonds : bond 0.04983 ( 353) hydrogen bonds : angle 4.94601 ( 975) link_BETA1-6 : bond 0.01076 ( 1) link_BETA1-6 : angle 1.73898 ( 3) SS BOND : bond 0.00848 ( 8) SS BOND : angle 1.14887 ( 16) covalent geometry : bond 0.00299 ( 8122) covalent geometry : angle 0.56511 (11027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.838 Fit side-chains REVERT: L 24 ARG cc_start: 0.6344 (mmm-85) cc_final: 0.6097 (tpp80) REVERT: H 43 GLN cc_start: 0.7388 (mm110) cc_final: 0.7037 (tt0) REVERT: A 95 LEU cc_start: 0.6281 (pp) cc_final: 0.4839 (tp) REVERT: A 111 ASP cc_start: 0.7279 (t0) cc_final: 0.6816 (m-30) REVERT: A 441 LYS cc_start: 0.7243 (tttt) cc_final: 0.7025 (ttpt) REVERT: A 455 MET cc_start: 0.7595 (tmm) cc_final: 0.7052 (ttp) outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 0.1972 time to fit residues: 34.5433 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS A 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153320 restraints weight = 9930.870| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.05 r_work: 0.3731 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 8137 Z= 0.201 Angle : 0.613 6.421 11064 Z= 0.319 Chirality : 0.044 0.172 1184 Planarity : 0.005 0.057 1410 Dihedral : 4.817 57.672 1205 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.30 % Allowed : 8.66 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 962 helix: 0.39 (0.26), residues: 375 sheet: 0.56 (0.41), residues: 148 loop : 0.04 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 117 HIS 0.005 0.001 HIS A 378 PHE 0.018 0.002 PHE A 438 TYR 0.027 0.002 TYR E 365 ARG 0.004 0.001 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 1.68780 ( 18) hydrogen bonds : bond 0.05350 ( 353) hydrogen bonds : angle 4.76441 ( 975) link_BETA1-6 : bond 0.00188 ( 1) link_BETA1-6 : angle 1.78587 ( 3) SS BOND : bond 0.00517 ( 8) SS BOND : angle 1.28952 ( 16) covalent geometry : bond 0.00467 ( 8122) covalent geometry : angle 0.60708 (11027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.842 Fit side-chains REVERT: L 24 ARG cc_start: 0.6665 (mmm-85) cc_final: 0.6420 (tpp80) REVERT: A 106 SER cc_start: 0.6239 (m) cc_final: 0.6017 (p) REVERT: A 423 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 441 LYS cc_start: 0.7409 (tttt) cc_final: 0.7139 (ttpt) REVERT: A 455 MET cc_start: 0.7710 (tmm) cc_final: 0.7343 (ttp) outliers start: 11 outliers final: 5 residues processed: 115 average time/residue: 0.1930 time to fit residues: 30.7729 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 228 HIS E 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154455 restraints weight = 9982.396| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.13 r_work: 0.3756 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8137 Z= 0.137 Angle : 0.552 8.329 11064 Z= 0.281 Chirality : 0.042 0.161 1184 Planarity : 0.004 0.054 1410 Dihedral : 4.626 58.088 1205 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.54 % Allowed : 9.49 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 962 helix: 0.60 (0.27), residues: 375 sheet: 0.46 (0.41), residues: 148 loop : 0.08 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 228 PHE 0.012 0.001 PHE A 438 TYR 0.015 0.001 TYR E 495 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 6) link_NAG-ASN : angle 1.70608 ( 18) hydrogen bonds : bond 0.04366 ( 353) hydrogen bonds : angle 4.54807 ( 975) link_BETA1-6 : bond 0.00275 ( 1) link_BETA1-6 : angle 1.66401 ( 3) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.01147 ( 16) covalent geometry : bond 0.00315 ( 8122) covalent geometry : angle 0.54648 (11027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.844 Fit side-chains REVERT: L 24 ARG cc_start: 0.6397 (mmm-85) cc_final: 0.6132 (tpp80) REVERT: H 43 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7226 (tt0) REVERT: H 82 GLU cc_start: 0.7756 (tt0) cc_final: 0.7532 (tt0) REVERT: A 423 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 441 LYS cc_start: 0.7372 (tttt) cc_final: 0.7073 (ttpt) REVERT: A 455 MET cc_start: 0.7623 (tmm) cc_final: 0.7314 (ttp) REVERT: A 470 LYS cc_start: 0.7798 (mttt) cc_final: 0.7465 (tttt) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.1937 time to fit residues: 30.3579 Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142281 restraints weight = 10010.142| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.09 r_work: 0.3603 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 8137 Z= 0.299 Angle : 0.735 9.368 11064 Z= 0.374 Chirality : 0.049 0.239 1184 Planarity : 0.006 0.058 1410 Dihedral : 5.548 59.079 1205 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.78 % Allowed : 10.68 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 962 helix: -0.16 (0.26), residues: 381 sheet: 0.26 (0.40), residues: 147 loop : -0.15 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 477 HIS 0.006 0.002 HIS L 92 PHE 0.026 0.003 PHE A 438 TYR 0.027 0.003 TYR A 587 ARG 0.005 0.001 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 6) link_NAG-ASN : angle 2.07637 ( 18) hydrogen bonds : bond 0.05921 ( 353) hydrogen bonds : angle 4.90195 ( 975) link_BETA1-6 : bond 0.00563 ( 1) link_BETA1-6 : angle 1.80153 ( 3) SS BOND : bond 0.00544 ( 8) SS BOND : angle 1.33461 ( 16) covalent geometry : bond 0.00720 ( 8122) covalent geometry : angle 0.72860 (11027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.6333 (tpp80) REVERT: H 43 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7308 (tt0) REVERT: H 82 GLU cc_start: 0.7872 (tt0) cc_final: 0.7647 (tt0) REVERT: A 106 SER cc_start: 0.6006 (m) cc_final: 0.5778 (p) REVERT: A 423 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 441 LYS cc_start: 0.7677 (tttt) cc_final: 0.7159 (ttpt) REVERT: A 479 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 610 TRP cc_start: 0.6662 (t60) cc_final: 0.6401 (t60) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.1901 time to fit residues: 30.5979 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 210 ASN A 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151616 restraints weight = 9888.837| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.04 r_work: 0.3722 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8137 Z= 0.147 Angle : 0.580 9.684 11064 Z= 0.292 Chirality : 0.042 0.198 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.999 58.675 1205 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.54 % Allowed : 11.51 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 962 helix: 0.29 (0.26), residues: 379 sheet: 0.41 (0.41), residues: 146 loop : -0.19 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.003 0.001 HIS A 228 PHE 0.013 0.001 PHE A 438 TYR 0.015 0.002 TYR E 495 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 1.98251 ( 18) hydrogen bonds : bond 0.04516 ( 353) hydrogen bonds : angle 4.60493 ( 975) link_BETA1-6 : bond 0.00047 ( 1) link_BETA1-6 : angle 1.66533 ( 3) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.89643 ( 16) covalent geometry : bond 0.00342 ( 8122) covalent geometry : angle 0.57414 (11027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6513 (mmm-85) cc_final: 0.6265 (tpp80) REVERT: H 82 GLU cc_start: 0.7858 (tt0) cc_final: 0.7614 (tt0) REVERT: A 423 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 441 LYS cc_start: 0.7513 (tttt) cc_final: 0.7006 (ttpt) REVERT: A 455 MET cc_start: 0.7691 (tmm) cc_final: 0.7334 (ttp) REVERT: A 479 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 610 TRP cc_start: 0.6813 (t60) cc_final: 0.6574 (t60) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1876 time to fit residues: 28.6095 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153550 restraints weight = 10027.002| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.12 r_work: 0.3750 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8137 Z= 0.114 Angle : 0.532 8.568 11064 Z= 0.269 Chirality : 0.041 0.167 1184 Planarity : 0.004 0.051 1410 Dihedral : 4.672 58.795 1205 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.54 % Allowed : 12.22 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 962 helix: 0.54 (0.27), residues: 382 sheet: 0.39 (0.42), residues: 148 loop : -0.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE E 456 TYR 0.012 0.001 TYR E 495 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.77769 ( 18) hydrogen bonds : bond 0.04038 ( 353) hydrogen bonds : angle 4.42093 ( 975) link_BETA1-6 : bond 0.00041 ( 1) link_BETA1-6 : angle 1.49357 ( 3) SS BOND : bond 0.00251 ( 8) SS BOND : angle 0.79579 ( 16) covalent geometry : bond 0.00254 ( 8122) covalent geometry : angle 0.52683 (11027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 GLU cc_start: 0.7907 (tt0) cc_final: 0.7693 (tt0) REVERT: A 423 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 441 LYS cc_start: 0.7444 (tttt) cc_final: 0.6881 (ttpt) REVERT: A 455 MET cc_start: 0.7655 (tmm) cc_final: 0.7345 (ttp) REVERT: A 479 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 610 TRP cc_start: 0.6810 (t60) cc_final: 0.6575 (t60) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.1972 time to fit residues: 30.4328 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150112 restraints weight = 10100.839| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.10 r_work: 0.3705 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8137 Z= 0.187 Angle : 0.607 8.298 11064 Z= 0.308 Chirality : 0.044 0.199 1184 Planarity : 0.005 0.053 1410 Dihedral : 5.004 57.483 1205 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.42 % Allowed : 12.57 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 962 helix: 0.44 (0.26), residues: 380 sheet: 0.36 (0.41), residues: 147 loop : -0.15 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.016 0.002 PHE A 438 TYR 0.020 0.002 TYR A 41 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 1.88970 ( 18) hydrogen bonds : bond 0.04815 ( 353) hydrogen bonds : angle 4.55006 ( 975) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.57679 ( 3) SS BOND : bond 0.00352 ( 8) SS BOND : angle 0.93489 ( 16) covalent geometry : bond 0.00440 ( 8122) covalent geometry : angle 0.60132 (11027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6507 (mmm-85) cc_final: 0.6194 (tpp80) REVERT: H 65 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 166 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 423 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 441 LYS cc_start: 0.7624 (tttt) cc_final: 0.7027 (ttpt) REVERT: A 455 MET cc_start: 0.7831 (tmm) cc_final: 0.7394 (ttp) REVERT: A 479 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 610 TRP cc_start: 0.6735 (t60) cc_final: 0.6489 (t60) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.1931 time to fit residues: 29.6731 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.176704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151520 restraints weight = 10108.839| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.04 r_work: 0.3719 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8137 Z= 0.145 Angle : 0.574 8.754 11064 Z= 0.290 Chirality : 0.042 0.191 1184 Planarity : 0.004 0.052 1410 Dihedral : 4.860 57.623 1205 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.42 % Allowed : 12.57 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 962 helix: 0.58 (0.27), residues: 379 sheet: 0.42 (0.42), residues: 147 loop : -0.16 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.004 0.001 HIS A 228 PHE 0.013 0.001 PHE A 438 TYR 0.015 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.84987 ( 18) hydrogen bonds : bond 0.04406 ( 353) hydrogen bonds : angle 4.48955 ( 975) link_BETA1-6 : bond 0.00202 ( 1) link_BETA1-6 : angle 1.53321 ( 3) SS BOND : bond 0.00307 ( 8) SS BOND : angle 1.06985 ( 16) covalent geometry : bond 0.00335 ( 8122) covalent geometry : angle 0.56811 (11027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6462 (mmm-85) cc_final: 0.6221 (tpp80) REVERT: H 82 GLU cc_start: 0.7847 (tt0) cc_final: 0.7564 (tt0) REVERT: A 166 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 423 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 441 LYS cc_start: 0.7514 (tttt) cc_final: 0.6943 (ttpt) REVERT: A 455 MET cc_start: 0.7740 (tmm) cc_final: 0.7368 (ttp) REVERT: A 479 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7427 (mt-10) outliers start: 12 outliers final: 11 residues processed: 108 average time/residue: 0.1921 time to fit residues: 29.1406 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.176358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151409 restraints weight = 9860.511| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.02 r_work: 0.3718 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8137 Z= 0.153 Angle : 0.584 9.010 11064 Z= 0.296 Chirality : 0.042 0.190 1184 Planarity : 0.004 0.052 1410 Dihedral : 4.862 57.455 1205 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.30 % Allowed : 12.81 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 962 helix: 0.60 (0.27), residues: 379 sheet: 0.43 (0.42), residues: 147 loop : -0.19 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.003 0.001 HIS L 92 PHE 0.013 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 6) link_NAG-ASN : angle 1.85615 ( 18) hydrogen bonds : bond 0.04476 ( 353) hydrogen bonds : angle 4.47750 ( 975) link_BETA1-6 : bond 0.00137 ( 1) link_BETA1-6 : angle 1.58314 ( 3) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.12421 ( 16) covalent geometry : bond 0.00356 ( 8122) covalent geometry : angle 0.57806 (11027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6459 (mmm-85) cc_final: 0.6214 (tpp80) REVERT: H 82 GLU cc_start: 0.7858 (tt0) cc_final: 0.7580 (tt0) REVERT: A 166 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6475 (tm-30) REVERT: A 423 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 441 LYS cc_start: 0.7516 (tttt) cc_final: 0.6946 (ttpt) REVERT: A 455 MET cc_start: 0.7717 (tmm) cc_final: 0.7351 (ttp) REVERT: A 610 TRP cc_start: 0.6960 (t60) cc_final: 0.6404 (t60) outliers start: 11 outliers final: 10 residues processed: 103 average time/residue: 0.1869 time to fit residues: 27.0083 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149934 restraints weight = 10022.328| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.03 r_work: 0.3704 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8137 Z= 0.177 Angle : 0.616 10.361 11064 Z= 0.311 Chirality : 0.044 0.208 1184 Planarity : 0.005 0.052 1410 Dihedral : 5.038 56.710 1205 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.42 % Allowed : 12.81 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 962 helix: 0.50 (0.27), residues: 380 sheet: 0.44 (0.42), residues: 147 loop : -0.21 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.004 0.001 HIS L 92 PHE 0.016 0.002 PHE A 438 TYR 0.019 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 6) link_NAG-ASN : angle 1.94429 ( 18) hydrogen bonds : bond 0.04766 ( 353) hydrogen bonds : angle 4.52400 ( 975) link_BETA1-6 : bond 0.00257 ( 1) link_BETA1-6 : angle 1.63064 ( 3) SS BOND : bond 0.00354 ( 8) SS BOND : angle 1.11274 ( 16) covalent geometry : bond 0.00418 ( 8122) covalent geometry : angle 0.61007 (11027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.57 seconds wall clock time: 67 minutes 43.21 seconds (4063.21 seconds total)