Starting phenix.real_space_refine on Fri Dec 27 11:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtw_37844/12_2024/8wtw_37844.cif" } resolution = 2.8 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= -0.001 sd= 0.053 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: 6 Type Number sf(0) Gaussians S 24 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3034 2.51 5 N 708 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4415 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 531} Chain breaks: 1 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 99 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0A1:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.77 Number of scatterers: 4531 At special positions: 0 Unit cell: (73.1, 68.85, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 24 16.00 Na 2 11.00 O 762 8.00 N 708 7.00 C 3034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 564.7 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 77.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.918A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.650A pdb=" N ARG A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.563A pdb=" N GLY A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.544A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.149A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 4.024A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.739A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.619A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.598A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.687A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.524A pdb=" N ARG A 301 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 303' Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.090A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.861A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 344 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.578A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 402 through 433 removed outlier: 3.511A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.641A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.784A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.528A pdb=" N MET A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.520A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.957A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.780A pdb=" N VAL A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.759A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.883A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 600 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.159A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 247 hydrogen bonds defined for protein. 720 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: 1.30 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 666 1.31 - 1.43: 1459 1.43 - 1.56: 2510 1.56 - 1.68: 2 1.68 - 1.81: 35 Bond restraints: 4672 Sorted by residual: bond pdb=" C ARG B 12 " pdb=" N HYP B 13 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.13e+00 bond pdb=" CZ 0A1 B 101 " pdb=" OH 0A1 B 101 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CA HYP B 13 " pdb=" C HYP B 13 " ideal model delta sigma weight residual 1.525 1.577 -0.052 2.10e-02 2.27e+03 6.04e+00 bond pdb=" C 0A1 B 101 " pdb=" O 0A1 B 101 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" CA ARG B 12 " pdb=" C ARG B 12 " ideal model delta sigma weight residual 1.525 1.573 -0.048 2.10e-02 2.27e+03 5.13e+00 ... (remaining 4667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6312 2.00 - 4.00: 39 4.00 - 5.99: 12 5.99 - 7.99: 0 7.99 - 9.99: 2 Bond angle restraints: 6365 Sorted by residual: angle pdb=" N HYP B 13 " pdb=" CA HYP B 13 " pdb=" CB HYP B 13 " ideal model delta sigma weight residual 103.00 108.02 -5.02 1.10e+00 8.26e-01 2.08e+01 angle pdb=" N HYP B 13 " pdb=" CD HYP B 13 " pdb=" CG HYP B 13 " ideal model delta sigma weight residual 103.20 108.53 -5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA 0A1 B 101 " pdb=" CB 0A1 B 101 " pdb=" CG 0A1 B 101 " ideal model delta sigma weight residual 118.13 109.10 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA CYS B 11 " pdb=" C CYS B 11 " pdb=" N ARG B 12 " ideal model delta sigma weight residual 116.01 113.08 2.93 1.49e+00 4.50e-01 3.88e+00 angle pdb=" CA ASP A 298 " pdb=" C ASP A 298 " pdb=" O ASP A 298 " ideal model delta sigma weight residual 120.47 118.04 2.43 1.35e+00 5.49e-01 3.25e+00 ... (remaining 6360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 2282 18.00 - 36.00: 256 36.00 - 54.00: 66 54.00 - 72.00: 8 72.00 - 90.00: 6 Dihedral angle restraints: 2618 sinusoidal: 989 harmonic: 1629 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -51.94 -34.06 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" CB GLU A 122 " pdb=" CG GLU A 122 " pdb=" CD GLU A 122 " pdb=" OE1 GLU A 122 " ideal model delta sinusoidal sigma weight residual 0.00 90.00 -90.00 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CG ARG A 440 " pdb=" CD ARG A 440 " pdb=" NE ARG A 440 " pdb=" CZ ARG A 440 " ideal model delta sinusoidal sigma weight residual -90.00 -133.70 43.70 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 2615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 375 0.023 - 0.046: 184 0.046 - 0.069: 110 0.069 - 0.092: 17 0.092 - 0.115: 21 Chirality restraints: 707 Sorted by residual: chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CG HYP B 13 " pdb=" CB HYP B 13 " pdb=" CD HYP B 13 " pdb=" OD1 HYP B 13 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.11 2.00e-01 2.50e+01 3.25e-01 chirality pdb=" CA PHE A 82 " pdb=" N PHE A 82 " pdb=" C PHE A 82 " pdb=" CB PHE A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 704 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 11 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C CYS B 11 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS B 11 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 12 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 107 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 108 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 512 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 513 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " -0.019 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1366 2.81 - 3.33: 3953 3.33 - 3.86: 6934 3.86 - 4.38: 8668 4.38 - 4.90: 14827 Nonbonded interactions: 35748 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 702 " model vdw 2.289 2.470 nonbonded pdb=" O GLY A 71 " pdb="NA NA A 703 " model vdw 2.305 2.470 nonbonded pdb=" O ARG A 442 " pdb=" OG1 THR A 446 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASN A 78 " pdb="NA NA A 702 " model vdw 2.318 2.470 nonbonded pdb=" O ILE A 349 " pdb=" OG1 THR A 353 " model vdw 2.319 3.040 ... (remaining 35743 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: 0.760 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4672 Z= 0.170 Angle : 0.477 9.989 6365 Z= 0.240 Chirality : 0.036 0.115 707 Planarity : 0.004 0.039 771 Dihedral : 16.197 90.005 1571 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 21.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.34), residues: 554 helix: -1.31 (0.24), residues: 361 sheet: 1.28 (2.52), residues: 6 loop : 0.55 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 599 PHE 0.018 0.001 PHE A 511 TYR 0.006 0.001 TYR A 575 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.496 Fit side-chains REVERT: A 377 GLU cc_start: 0.7801 (mp0) cc_final: 0.7172 (mp0) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 1.0128 time to fit residues: 56.6093 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 chunk 23 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4672 Z= 0.149 Angle : 0.505 7.663 6365 Z= 0.270 Chirality : 0.039 0.153 707 Planarity : 0.004 0.033 771 Dihedral : 4.009 38.957 613 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.95 % Allowed : 20.00 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.37), residues: 554 helix: 0.43 (0.27), residues: 379 sheet: 0.43 (2.09), residues: 6 loop : 0.65 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.013 0.001 PHE A 403 TYR 0.008 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.511 Fit side-chains REVERT: A 391 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 607 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7720 (ttm170) outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.9243 time to fit residues: 48.9780 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 607 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4672 Z= 0.194 Angle : 0.512 9.121 6365 Z= 0.269 Chirality : 0.040 0.149 707 Planarity : 0.004 0.034 771 Dihedral : 4.089 38.559 613 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.95 % Allowed : 19.79 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.37), residues: 554 helix: 0.92 (0.28), residues: 380 sheet: 0.20 (1.83), residues: 6 loop : 0.56 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.003 0.000 HIS A 599 PHE 0.015 0.001 PHE A 362 TYR 0.012 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.530 Fit side-chains REVERT: A 391 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 607 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7823 (ttm170) outliers start: 14 outliers final: 8 residues processed: 47 average time/residue: 1.0232 time to fit residues: 50.9220 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 607 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4672 Z= 0.186 Angle : 0.498 9.560 6365 Z= 0.260 Chirality : 0.039 0.149 707 Planarity : 0.004 0.033 771 Dihedral : 4.143 39.231 613 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.95 % Allowed : 20.63 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.38), residues: 554 helix: 1.06 (0.28), residues: 386 sheet: None (None), residues: 0 loop : 0.38 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 264 HIS 0.002 0.000 HIS A 599 PHE 0.013 0.001 PHE A 362 TYR 0.011 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.483 Fit side-chains REVERT: A 391 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7581 (m-80) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.9776 time to fit residues: 51.5935 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4672 Z= 0.115 Angle : 0.435 7.615 6365 Z= 0.226 Chirality : 0.037 0.152 707 Planarity : 0.003 0.029 771 Dihedral : 3.884 37.989 613 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.53 % Allowed : 21.68 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.38), residues: 554 helix: 1.35 (0.28), residues: 386 sheet: None (None), residues: 0 loop : 0.50 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.009 0.001 TYR A 572 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.535 Fit side-chains REVERT: A 391 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7713 (m-80) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 1.0082 time to fit residues: 54.2783 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4672 Z= 0.186 Angle : 0.489 9.515 6365 Z= 0.255 Chirality : 0.039 0.150 707 Planarity : 0.004 0.031 771 Dihedral : 4.048 38.240 613 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 21.89 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.38), residues: 554 helix: 1.24 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.36 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.002 0.001 HIS A 599 PHE 0.014 0.001 PHE A 362 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.505 Fit side-chains REVERT: A 391 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7611 (m-80) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 1.0463 time to fit residues: 51.9109 Evaluate side-chains 44 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4672 Z= 0.192 Angle : 0.498 9.998 6365 Z= 0.259 Chirality : 0.040 0.150 707 Planarity : 0.004 0.032 771 Dihedral : 4.185 39.152 613 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 21.47 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.38), residues: 554 helix: 1.22 (0.28), residues: 391 sheet: None (None), residues: 0 loop : 0.33 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.002 0.000 HIS A 599 PHE 0.013 0.001 PHE A 362 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.534 Fit side-chains REVERT: A 391 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7534 (m-80) outliers start: 13 outliers final: 7 residues processed: 46 average time/residue: 0.8896 time to fit residues: 43.5287 Evaluate side-chains 43 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4672 Z= 0.127 Angle : 0.451 8.393 6365 Z= 0.234 Chirality : 0.038 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.997 38.635 613 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.26 % Allowed : 22.53 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.38), residues: 554 helix: 1.37 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.47 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.001 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.471 Fit side-chains REVERT: A 391 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7611 (m-80) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.8893 time to fit residues: 42.9484 Evaluate side-chains 44 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.002 0.030 4672 Z= 0.132 Angle : 0.451 8.370 6365 Z= 0.234 Chirality : 0.038 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.939 37.899 613 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.32 % Allowed : 21.68 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.38), residues: 554 helix: 1.41 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.51 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.512 Fit side-chains REVERT: A 391 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7612 (m-80) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.8258 time to fit residues: 41.5299 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4672 Z= 0.119 Angle : 0.436 7.813 6365 Z= 0.225 Chirality : 0.038 0.152 707 Planarity : 0.003 0.029 771 Dihedral : 3.831 37.114 613 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.47 % Allowed : 22.53 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.38), residues: 554 helix: 1.49 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.58 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.009 0.001 TYR A 572 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.514 Fit side-chains REVERT: A 110 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: A 391 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7668 (m-80) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.9111 time to fit residues: 42.5156 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120004 restraints weight = 5580.491| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.55 r_work: 0.3230 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4672 Z= 0.115 Angle : 0.432 7.802 6365 Z= 0.223 Chirality : 0.038 0.152 707 Planarity : 0.003 0.028 771 Dihedral : 3.746 36.340 613 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.68 % Allowed : 22.53 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.38), residues: 554 helix: 1.57 (0.28), residues: 388 sheet: None (None), residues: 0 loop : 0.58 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.009 0.001 TYR A 572 ARG 0.001 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.76 seconds wall clock time: 30 minutes 42.67 seconds (1842.67 seconds total)