Starting phenix.real_space_refine on Thu Oct 10 17:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iuz_60916/10_2024/9iuz_60916.cif" } resolution = 3.19 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= 0.022 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 65 5.16 5 C 5286 2.51 5 N 1443 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8349 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4171 Classifications: {'peptide': 537} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 514} Chain breaks: 4 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 384 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.63 Number of scatterers: 8349 At special positions: 0 Unit cell: (73.95, 120.7, 119, 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 65 16.00 O 1555 8.00 N 1443 7.00 C 5286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 46.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 55 through 77 removed outlier: 3.566A pdb=" N GLN B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.649A pdb=" N ILE B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 223 through 247 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 411 through 458 removed outlier: 4.099A pdb=" N ARG B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.567A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.512A pdb=" N GLY B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.568A pdb=" N GLU B 560 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 600 through 621 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.626A pdb=" N MET A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.557A pdb=" N SER A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 457 removed outlier: 3.714A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.510A pdb=" N ILE A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.840A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 533' Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'C' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 114 removed outlier: 4.007A pdb=" N TYR B 133 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 122 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 133 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET B 120 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.670A pdb=" N TYR B 303 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 284 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 275 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU B 289 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 273 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET B 394 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B 379 " --> pdb=" O MET B 394 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 396 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 377 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 398 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 486 through 491 removed outlier: 3.742A pdb=" N PHE B 481 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 478 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 549 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 539 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.513A pdb=" N TYR A 133 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET A 120 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 206 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 192 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.626A pdb=" N TYR A 303 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 491 removed outlier: 3.602A pdb=" N GLY A 478 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 554 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 451 hydrogen bonds defined for protein. 1245 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: 2.37 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1957 1.33 - 1.45: 1713 1.45 - 1.57: 4736 1.57 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 8513 Sorted by residual: bond pdb=" N ILE B 499 " pdb=" CA ILE B 499 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.21e-02 6.83e+03 5.81e+00 bond pdb=" CAC O6E B1001 " pdb=" CAH O6E B1001 " ideal model delta sigma weight residual 1.522 1.561 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" N LEU B 87 " pdb=" CA LEU B 87 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.51e+00 bond pdb=" N MET B 439 " pdb=" CA MET B 439 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.18e+00 bond pdb=" N MET B 431 " pdb=" CA MET B 431 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.75e+00 ... (remaining 8508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11390 2.25 - 4.51: 113 4.51 - 6.76: 10 6.76 - 9.01: 3 9.01 - 11.27: 2 Bond angle restraints: 11518 Sorted by residual: angle pdb=" CAH O6E B1001 " pdb=" CAC O6E B1001 " pdb=" CBJ O6E B1001 " ideal model delta sigma weight residual 112.38 101.11 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C GLN B 498 " pdb=" N ILE B 499 " pdb=" CA ILE B 499 " ideal model delta sigma weight residual 120.42 115.98 4.44 1.42e+00 4.96e-01 9.76e+00 angle pdb=" N LYS A 546 " pdb=" CA LYS A 546 " pdb=" C LYS A 546 " ideal model delta sigma weight residual 114.75 110.83 3.92 1.26e+00 6.30e-01 9.70e+00 angle pdb=" CB MET B 422 " pdb=" CG MET B 422 " pdb=" SD MET B 422 " ideal model delta sigma weight residual 112.70 121.85 -9.15 3.00e+00 1.11e-01 9.31e+00 angle pdb=" C ASN B 430 " pdb=" N MET B 431 " pdb=" CA MET B 431 " ideal model delta sigma weight residual 120.44 116.56 3.88 1.30e+00 5.92e-01 8.93e+00 ... (remaining 11513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4360 18.00 - 36.00: 604 36.00 - 53.99: 163 53.99 - 71.99: 27 71.99 - 89.99: 16 Dihedral angle restraints: 5170 sinusoidal: 2104 harmonic: 3066 Sorted by residual: dihedral pdb=" CA LEU A 550 " pdb=" C LEU A 550 " pdb=" N PHE A 551 " pdb=" CA PHE A 551 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 -87.38 87.38 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 504 " pdb=" CG GLU A 504 " pdb=" CD GLU A 504 " pdb=" OE1 GLU A 504 " ideal model delta sinusoidal sigma weight residual 0.00 -87.30 87.30 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 942 0.037 - 0.075: 248 0.075 - 0.112: 79 0.112 - 0.150: 20 0.150 - 0.187: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CG LEU A 507 " pdb=" CB LEU A 507 " pdb=" CD1 LEU A 507 " pdb=" CD2 LEU A 507 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ASP A 209 " pdb=" N ASP A 209 " pdb=" C ASP A 209 " pdb=" CB ASP A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1287 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 580 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO A 581 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 505 " 0.014 2.00e-02 2.50e+03 1.44e-02 5.18e+00 pdb=" CG TRP A 505 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 505 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 505 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 505 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 505 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 505 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 505 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 505 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 505 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 580 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 581 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1306 2.76 - 3.30: 7834 3.30 - 3.83: 13394 3.83 - 4.37: 14410 4.37 - 4.90: 26089 Nonbonded interactions: 63033 Sorted by model distance: nonbonded pdb=" O VAL A 264 " pdb=" OG1 THR A 268 " model vdw 2.226 3.040 nonbonded pdb=" O ASP B 82 " pdb=" OG SER B 86 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 45 " pdb=" OD2 ASP C 48 " model vdw 2.256 3.040 nonbonded pdb=" O LEU A 614 " pdb=" OG SER A 617 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 495 " pdb=" OE1 GLN A 498 " model vdw 2.259 3.040 ... (remaining 63028 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 111 through 144 or resid 156 through 565 or resid 577 thro \ ugh 621 or resid 1001)) } 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: 0.610 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.220 Find NCS groups from input model: 0.340 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 : 0.002 0.039 8513 Z= 0.170 Angle : 0.562 11.268 11518 Z= 0.297 Chirality : 0.039 0.187 1290 Planarity : 0.004 0.060 1477 Dihedral : 18.043 89.989 3186 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.55 % Allowed : 30.60 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.40 (0.27), residues: 1039 helix: 2.89 (0.25), residues: 418 sheet: 0.13 (0.38), residues: 188 loop : -0.70 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 505 HIS 0.003 0.001 HIS B 206 PHE 0.009 0.001 PHE C 58 TYR 0.019 0.001 TYR B 487 ARG 0.007 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8585 (ttp) cc_final: 0.8323 (ttp) REVERT: B 595 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6591 (ttp-170) REVERT: A 159 MET cc_start: 0.7503 (mmt) cc_final: 0.7229 (tpt) REVERT: A 266 ASP cc_start: 0.8861 (t0) cc_final: 0.8568 (t0) REVERT: A 594 SER cc_start: 0.8005 (m) cc_final: 0.7728 (p) REVERT: C 30 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8411 (pttm) outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.2034 time to fit residues: 37.7508 Evaluate side-chains 124 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 318 GLN A 336 GLN A 358 HIS A 403 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8513 Z= 0.262 Angle : 0.574 7.802 11518 Z= 0.295 Chirality : 0.041 0.144 1290 Planarity : 0.004 0.058 1477 Dihedral : 5.438 70.729 1232 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.44 % Allowed : 26.39 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.19 (0.27), residues: 1039 helix: 2.70 (0.25), residues: 426 sheet: -0.12 (0.38), residues: 192 loop : -0.79 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 505 HIS 0.004 0.001 HIS B 302 PHE 0.008 0.002 PHE B 314 TYR 0.017 0.002 TYR B 487 ARG 0.004 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8506 (ttp) cc_final: 0.8263 (ttp) REVERT: B 595 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7032 (ttp-170) REVERT: A 159 MET cc_start: 0.7626 (mmt) cc_final: 0.7394 (tpt) REVERT: A 266 ASP cc_start: 0.8884 (t0) cc_final: 0.8623 (t0) REVERT: A 368 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 416 TYR cc_start: 0.7621 (m-80) cc_final: 0.7416 (m-80) REVERT: A 594 SER cc_start: 0.8112 (m) cc_final: 0.7823 (p) REVERT: C 30 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8362 (ttpt) outliers start: 31 outliers final: 17 residues processed: 151 average time/residue: 0.2120 time to fit residues: 43.7358 Evaluate side-chains 133 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 584 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN A 188 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8513 Z= 0.163 Angle : 0.519 7.867 11518 Z= 0.264 Chirality : 0.039 0.146 1290 Planarity : 0.004 0.057 1477 Dihedral : 4.937 70.373 1226 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.77 % Allowed : 26.50 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.36 (0.27), residues: 1039 helix: 2.90 (0.25), residues: 425 sheet: 0.03 (0.38), residues: 188 loop : -0.79 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 PHE 0.006 0.001 PHE B 117 TYR 0.013 0.001 TYR B 487 ARG 0.004 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 595 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6961 (ttp-170) REVERT: A 159 MET cc_start: 0.7545 (mmt) cc_final: 0.7325 (tpt) REVERT: A 303 TYR cc_start: 0.8740 (p90) cc_final: 0.8322 (p90) REVERT: A 368 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8275 (mm) REVERT: A 594 SER cc_start: 0.7999 (m) cc_final: 0.7733 (p) REVERT: C 30 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8355 (ttpt) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 0.2028 time to fit residues: 40.6206 Evaluate side-chains 128 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 319 ASN B 355 HIS A 188 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8513 Z= 0.413 Angle : 0.648 8.332 11518 Z= 0.328 Chirality : 0.043 0.172 1290 Planarity : 0.005 0.056 1477 Dihedral : 5.764 72.677 1226 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.66 % Allowed : 25.06 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.27), residues: 1039 helix: 2.44 (0.25), residues: 426 sheet: -0.36 (0.37), residues: 199 loop : -0.97 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 505 HIS 0.005 0.001 HIS B 302 PHE 0.038 0.002 PHE A 618 TYR 0.021 0.002 TYR B 487 ARG 0.006 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7917 (mtt) cc_final: 0.7590 (ttm) REVERT: B 295 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 431 MET cc_start: 0.8087 (ttp) cc_final: 0.7851 (ttp) REVERT: B 595 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6981 (ttp-170) REVERT: A 159 MET cc_start: 0.7762 (mmt) cc_final: 0.6848 (tpt) REVERT: A 303 TYR cc_start: 0.8865 (p90) cc_final: 0.8506 (p90) REVERT: A 368 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 594 SER cc_start: 0.8204 (m) cc_final: 0.7952 (p) REVERT: C 30 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8243 (ttpp) outliers start: 42 outliers final: 31 residues processed: 150 average time/residue: 0.2063 time to fit residues: 42.7496 Evaluate side-chains 147 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8513 Z= 0.146 Angle : 0.531 8.936 11518 Z= 0.267 Chirality : 0.039 0.166 1290 Planarity : 0.004 0.057 1477 Dihedral : 5.153 72.909 1226 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.44 % Allowed : 28.49 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.29 (0.27), residues: 1039 helix: 2.87 (0.25), residues: 426 sheet: -0.15 (0.37), residues: 196 loop : -0.81 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 PHE 0.009 0.001 PHE A 618 TYR 0.020 0.001 TYR B 487 ARG 0.005 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7833 (mtt) cc_final: 0.7570 (ttm) REVERT: B 595 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6981 (ttp-170) REVERT: A 159 MET cc_start: 0.7702 (mmt) cc_final: 0.7489 (tpt) REVERT: A 594 SER cc_start: 0.8053 (m) cc_final: 0.7780 (p) REVERT: C 30 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8296 (ttpp) outliers start: 22 outliers final: 14 residues processed: 144 average time/residue: 0.2028 time to fit residues: 40.8503 Evaluate side-chains 133 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8513 Z= 0.253 Angle : 0.579 8.550 11518 Z= 0.290 Chirality : 0.041 0.151 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.331 74.368 1226 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.10 % Allowed : 27.94 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.27), residues: 1039 helix: 2.76 (0.25), residues: 427 sheet: -0.29 (0.37), residues: 197 loop : -0.92 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 PHE 0.009 0.002 PHE B 549 TYR 0.021 0.001 TYR B 487 ARG 0.011 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 595 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7014 (ttp-170) REVERT: A 159 MET cc_start: 0.7776 (mmt) cc_final: 0.7562 (tpt) REVERT: A 548 ASP cc_start: 0.5428 (OUTLIER) cc_final: 0.5041 (m-30) REVERT: A 594 SER cc_start: 0.8103 (m) cc_final: 0.7856 (p) REVERT: C 30 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8310 (ttpp) outliers start: 28 outliers final: 19 residues processed: 142 average time/residue: 0.1913 time to fit residues: 38.3742 Evaluate side-chains 137 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8513 Z= 0.298 Angle : 0.606 8.721 11518 Z= 0.304 Chirality : 0.041 0.148 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.475 73.553 1226 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.55 % Allowed : 26.50 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.95 (0.27), residues: 1039 helix: 2.60 (0.25), residues: 427 sheet: -0.45 (0.36), residues: 208 loop : -0.95 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 505 HIS 0.005 0.001 HIS B 283 PHE 0.038 0.002 PHE A 618 TYR 0.022 0.002 TYR B 487 ARG 0.003 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7903 (mtt) cc_final: 0.7608 (ttm) REVERT: B 265 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7742 (ttt90) REVERT: B 595 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7043 (ttp-170) REVERT: A 140 MET cc_start: 0.7897 (ptm) cc_final: 0.7598 (ppp) REVERT: A 548 ASP cc_start: 0.5413 (OUTLIER) cc_final: 0.5151 (m-30) REVERT: A 594 SER cc_start: 0.8160 (m) cc_final: 0.7898 (p) REVERT: C 30 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8234 (ttpp) outliers start: 41 outliers final: 25 residues processed: 151 average time/residue: 0.1956 time to fit residues: 41.3946 Evaluate side-chains 144 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8513 Z= 0.171 Angle : 0.557 8.715 11518 Z= 0.279 Chirality : 0.039 0.131 1290 Planarity : 0.004 0.056 1477 Dihedral : 5.158 74.189 1226 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.99 % Allowed : 27.83 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.19 (0.27), residues: 1039 helix: 2.89 (0.25), residues: 420 sheet: -0.28 (0.36), residues: 205 loop : -0.89 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 505 HIS 0.004 0.001 HIS A 283 PHE 0.013 0.001 PHE A 551 TYR 0.021 0.001 TYR B 487 ARG 0.004 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7876 (mtt) cc_final: 0.7625 (ttm) REVERT: B 595 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7041 (ttp-170) REVERT: A 548 ASP cc_start: 0.5268 (OUTLIER) cc_final: 0.5001 (m-30) REVERT: A 594 SER cc_start: 0.8036 (m) cc_final: 0.7763 (p) REVERT: C 30 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8262 (ttpp) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.1978 time to fit residues: 40.9309 Evaluate side-chains 143 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8513 Z= 0.279 Angle : 0.613 9.412 11518 Z= 0.307 Chirality : 0.042 0.283 1290 Planarity : 0.004 0.054 1477 Dihedral : 5.436 74.420 1226 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.99 % Allowed : 28.05 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.02 (0.27), residues: 1039 helix: 2.72 (0.25), residues: 421 sheet: -0.41 (0.36), residues: 207 loop : -0.94 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 505 HIS 0.005 0.001 HIS B 206 PHE 0.017 0.002 PHE A 551 TYR 0.018 0.002 TYR B 487 ARG 0.002 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7934 (mtt) cc_final: 0.7674 (ttm) REVERT: B 595 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7090 (ttp-170) REVERT: A 548 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.5042 (m-30) REVERT: A 594 SER cc_start: 0.8080 (m) cc_final: 0.7848 (p) REVERT: C 30 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8360 (ttpt) outliers start: 27 outliers final: 25 residues processed: 143 average time/residue: 0.1942 time to fit residues: 38.7846 Evaluate side-chains 146 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8513 Z= 0.165 Angle : 0.565 9.359 11518 Z= 0.282 Chirality : 0.040 0.287 1290 Planarity : 0.004 0.056 1477 Dihedral : 5.133 75.495 1226 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.33 % Allowed : 28.94 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.23 (0.27), residues: 1039 helix: 2.90 (0.25), residues: 420 sheet: -0.26 (0.37), residues: 205 loop : -0.86 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 505 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE C 58 TYR 0.018 0.001 TYR B 487 ARG 0.002 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: B 159 MET cc_start: 0.7877 (mtt) cc_final: 0.7669 (ttm) REVERT: B 235 GLN cc_start: 0.8318 (tp40) cc_final: 0.7974 (tp40) REVERT: B 595 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7089 (ttp-170) REVERT: A 548 ASP cc_start: 0.5362 (OUTLIER) cc_final: 0.4984 (m-30) REVERT: A 594 SER cc_start: 0.7962 (m) cc_final: 0.7708 (p) REVERT: C 30 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8271 (ttpt) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.2017 time to fit residues: 41.0187 Evaluate side-chains 138 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 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 = 0.3981 r_free = 0.3981 target = 0.136799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102024 restraints weight = 13741.574| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.86 r_work: 0.3344 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8513 Z= 0.209 Angle : 0.584 9.467 11518 Z= 0.291 Chirality : 0.041 0.275 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.248 75.231 1226 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.66 % Allowed : 28.82 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.20 (0.27), residues: 1039 helix: 2.87 (0.25), residues: 420 sheet: -0.26 (0.37), residues: 205 loop : -0.86 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 PHE 0.018 0.002 PHE C 58 TYR 0.019 0.001 TYR B 487 ARG 0.003 0.000 ARG A 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.34 seconds wall clock time: 36 minutes 20.40 seconds (2180.40 seconds total)