Starting phenix.real_space_refine on Fri Nov 15 01:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_29530.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_29530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_29530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_29530.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxb_29530/11_2024/8fxb_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.86, per 1000 atoms: 0.61 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: 2.28 Conformation dependent library (CDL) restraints added in 995.2 milliseconds 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: 0.98 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: 2.32 Time building geometry restraints manager: 2.54 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: 0.860 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- 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 0.059 8122 Z= 0.721 Angle : 1.210 12.604 11027 Z= 0.841 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 *********************** 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 : 0.832 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: 0.1766 time to fit residues: 43.3964 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 : 0.809 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 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 8122 Z= 0.191 Angle : 0.565 7.809 11027 Z= 0.300 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 *********************** 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 : 0.877 Fit side-chains REVERT: A 95 LEU cc_start: 0.6225 (pp) cc_final: 0.4910 (tp) REVERT: A 455 MET cc_start: 0.7289 (tmm) cc_final: 0.6831 (ttp) outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 0.2086 time to fit residues: 36.4932 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 48 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 E 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8122 Z= 0.270 Angle : 0.578 6.133 11027 Z= 0.302 Chirality : 0.043 0.164 1184 Planarity : 0.005 0.056 1410 Dihedral : 4.677 57.294 1205 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 0.35 (0.27), residues: 962 helix: 0.47 (0.26), residues: 379 sheet: 0.62 (0.41), residues: 148 loop : 0.04 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 117 HIS 0.005 0.001 HIS A 378 PHE 0.016 0.002 PHE A 438 TYR 0.027 0.002 TYR E 365 ARG 0.004 0.000 ARG A 460 *********************** 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 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.908 Fit side-chains REVERT: A 423 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7615 (mp) REVERT: A 455 MET cc_start: 0.7417 (tmm) cc_final: 0.7132 (ttp) outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 0.2033 time to fit residues: 33.1498 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 E residue 456 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8122 Z= 0.213 Angle : 0.550 8.238 11027 Z= 0.281 Chirality : 0.042 0.160 1184 Planarity : 0.004 0.054 1410 Dihedral : 4.622 57.928 1205 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.30 % Allowed : 10.08 % Favored : 88.61 % 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: 0.50 (0.40), residues: 147 loop : 0.08 (0.31), residues: 440 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 0.013 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.003 0.000 ARG A 460 *********************** 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: 11 poor density : 105 time to evaluate : 0.943 Fit side-chains REVERT: H 82 GLU cc_start: 0.7053 (tt0) cc_final: 0.6797 (tt0) REVERT: A 455 MET cc_start: 0.7382 (tmm) cc_final: 0.7150 (ttp) outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 0.1975 time to fit residues: 31.1226 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 433 GLU Chi-restraints excluded: chain A residue 491 VAL 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 52 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 E 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 8122 Z= 0.546 Angle : 0.791 10.245 11027 Z= 0.405 Chirality : 0.051 0.254 1184 Planarity : 0.006 0.060 1410 Dihedral : 5.872 58.062 1205 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.02 % Allowed : 11.15 % Favored : 86.83 % 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: -0.46 (0.26), residues: 962 helix: -0.36 (0.25), residues: 380 sheet: 0.18 (0.39), residues: 147 loop : -0.24 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 168 HIS 0.007 0.002 HIS A 378 PHE 0.029 0.003 PHE A 438 TYR 0.032 0.003 TYR A 587 ARG 0.005 0.001 ARG A 460 *********************** 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: 17 poor density : 101 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: H 82 GLU cc_start: 0.7125 (tt0) cc_final: 0.6848 (tt0) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.1876 time to fit residues: 30.5293 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain A residue 95 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 433 GLU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 491 VAL 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 83 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 E 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8122 Z= 0.203 Angle : 0.580 9.913 11027 Z= 0.295 Chirality : 0.042 0.195 1184 Planarity : 0.004 0.053 1410 Dihedral : 5.046 58.162 1205 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.42 % Allowed : 11.98 % Favored : 86.60 % 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: 0.02 (0.27), residues: 962 helix: 0.25 (0.26), residues: 381 sheet: 0.36 (0.40), residues: 146 loop : -0.18 (0.31), residues: 435 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 0.012 0.001 PHE A 438 TYR 0.015 0.002 TYR A 41 ARG 0.004 0.000 ARG L 46 *********************** 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: 12 poor density : 102 time to evaluate : 0.738 Fit side-chains REVERT: A 455 MET cc_start: 0.7439 (tmm) cc_final: 0.7139 (ttp) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.2065 time to fit residues: 31.3702 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain A residue 95 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 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 10 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 239 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 8122 Z= 0.390 Angle : 0.681 10.327 11027 Z= 0.347 Chirality : 0.046 0.230 1184 Planarity : 0.005 0.057 1410 Dihedral : 5.467 56.243 1205 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.54 % Allowed : 12.69 % 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: -0.23 (0.26), residues: 962 helix: -0.03 (0.26), residues: 382 sheet: 0.25 (0.41), residues: 147 loop : -0.25 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 477 HIS 0.005 0.002 HIS L 92 PHE 0.022 0.002 PHE A 438 TYR 0.024 0.002 TYR A 41 ARG 0.004 0.001 ARG A 460 *********************** 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 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 0.1944 time to fit residues: 28.5288 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain A residue 95 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 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 27 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8122 Z= 0.194 Angle : 0.566 9.040 11027 Z= 0.288 Chirality : 0.042 0.193 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.995 56.455 1205 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.54 % Allowed : 12.57 % 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: 0.07 (0.27), residues: 962 helix: 0.41 (0.26), residues: 381 sheet: 0.27 (0.41), residues: 148 loop : -0.21 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.012 0.001 PHE A 438 TYR 0.014 0.001 TYR E 495 ARG 0.004 0.000 ARG L 46 *********************** 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 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 455 MET cc_start: 0.7466 (tmm) cc_final: 0.7150 (ttp) REVERT: A 610 TRP cc_start: 0.6929 (t60) cc_final: 0.6605 (t60) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.1778 time to fit residues: 27.0322 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 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 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 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8122 Z= 0.225 Angle : 0.577 9.142 11027 Z= 0.292 Chirality : 0.042 0.189 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.928 56.047 1205 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.30 % Allowed : 13.05 % Favored : 85.65 % 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: 0.18 (0.27), residues: 962 helix: 0.53 (0.26), residues: 381 sheet: 0.44 (0.42), residues: 146 loop : -0.23 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.012 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 *********************** 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 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 455 MET cc_start: 0.7450 (tmm) cc_final: 0.7136 (ttp) REVERT: A 610 TRP cc_start: 0.6959 (t60) cc_final: 0.6628 (t60) outliers start: 11 outliers final: 11 residues processed: 104 average time/residue: 0.1931 time to fit residues: 28.2724 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 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 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 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8122 Z= 0.232 Angle : 0.579 8.982 11027 Z= 0.293 Chirality : 0.042 0.189 1184 Planarity : 0.004 0.052 1410 Dihedral : 4.900 55.577 1205 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.07 % Allowed : 13.29 % Favored : 85.65 % 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: 0.22 (0.27), residues: 962 helix: 0.57 (0.26), residues: 381 sheet: 0.42 (0.42), residues: 147 loop : -0.21 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.013 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 ********************** 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 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 455 MET cc_start: 0.7456 (tmm) cc_final: 0.7141 (ttp) REVERT: A 610 TRP cc_start: 0.6952 (t60) cc_final: 0.6624 (t60) outliers start: 9 outliers final: 9 residues processed: 96 average time/residue: 0.1965 time to fit residues: 26.7493 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 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 324 THR Chi-restraints excluded: chain A residue 468 ILE 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 23 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149434 restraints weight = 9907.404| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.01 r_work: 0.3695 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8122 Z= 0.293 Angle : 0.626 11.580 11027 Z= 0.315 Chirality : 0.044 0.208 1184 Planarity : 0.005 0.053 1410 Dihedral : 5.104 54.895 1205 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.30 % Allowed : 13.29 % Favored : 85.41 % 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: 0.11 (0.27), residues: 962 helix: 0.43 (0.26), residues: 381 sheet: 0.50 (0.42), residues: 146 loop : -0.27 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 275 HIS 0.004 0.001 HIS A 239 PHE 0.016 0.002 PHE A 438 TYR 0.019 0.002 TYR E 495 ARG 0.004 0.001 ARG L 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.02 seconds wall clock time: 32 minutes 19.96 seconds (1939.96 seconds total)