Starting phenix.real_space_refine on Sat Nov 16 17:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/11_2024/8hfy_34728.cif" } resolution = 3.21 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4195 2.51 5 N 1075 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.82, per 1000 atoms: 0.89 Number of scatterers: 6568 At special positions: 0 Unit cell: (85, 88.4, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1259 8.00 N 1075 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 701 " - " ASN A 432 " " NAG A 702 " - " ASN A 299 " " NAG A 703 " - " ASN A 91 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 962.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 54.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.749A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.508A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.677A pdb=" N HIS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.724A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.559A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.243A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.585A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 removed outlier: 3.831A pdb=" N GLN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.705A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.959A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.647A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.110A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.948A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.909A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.687A pdb=" N ARG A 393 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.136A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.194A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.575A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.047A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.626A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.114A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.368A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 843 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: 1.79 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2075 1.34 - 1.46: 1522 1.46 - 1.58: 3091 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6748 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.444 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8936 1.56 - 3.13: 179 3.13 - 4.69: 32 4.69 - 6.25: 7 6.25 - 7.82: 2 Bond angle restraints: 9156 Sorted by residual: angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 106.55 110.56 -4.01 1.45e+00 4.76e-01 7.66e+00 angle pdb=" C PHE B 375 " pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 122.41 118.51 3.90 1.47e+00 4.63e-01 7.04e+00 angle pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sigma weight residual 113.21 121.03 -7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 118.46 4.19 1.66e+00 3.63e-01 6.36e+00 angle pdb=" N GLY A 537 " pdb=" CA GLY A 537 " pdb=" C GLY A 537 " ideal model delta sigma weight residual 110.46 113.97 -3.51 1.43e+00 4.89e-01 6.04e+00 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 3926 24.82 - 49.64: 135 49.64 - 74.46: 18 74.46 - 99.28: 14 99.28 - 124.10: 15 Dihedral angle restraints: 4108 sinusoidal: 1778 harmonic: 2330 Sorted by residual: dihedral pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual -62.96 61.14 -124.10 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 173.99 114.72 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -65.53 113.15 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 4105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 812 0.053 - 0.107: 146 0.107 - 0.160: 19 0.160 - 0.214: 1 0.214 - 0.267: 1 Chirality restraints: 979 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.58e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.48e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 976 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 373 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 444 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C LEU A 444 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 444 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 445 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 146 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.021 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 68 2.64 - 3.21: 5868 3.21 - 3.77: 9628 3.77 - 4.34: 13493 4.34 - 4.90: 22737 Nonbonded interactions: 51794 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 704 " model vdw 2.081 2.230 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR A 42 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.257 3.040 ... (remaining 51789 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.073 6748 Z= 0.194 Angle : 0.554 7.817 9156 Z= 0.288 Chirality : 0.042 0.267 979 Planarity : 0.004 0.049 1166 Dihedral : 15.549 124.095 2600 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 6.47 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 785 helix: 1.41 (0.27), residues: 392 sheet: 0.52 (0.80), residues: 44 loop : -1.30 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7229 (t0) cc_final: 0.6988 (t0) REVERT: A 149 ASP cc_start: 0.8409 (t0) cc_final: 0.8204 (t0) REVERT: A 152 MET cc_start: 0.9148 (mmm) cc_final: 0.8644 (mmt) outliers start: 10 outliers final: 3 residues processed: 130 average time/residue: 0.2219 time to fit residues: 36.7284 Evaluate side-chains 76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6748 Z= 0.272 Angle : 0.627 10.860 9156 Z= 0.315 Chirality : 0.044 0.219 979 Planarity : 0.005 0.055 1166 Dihedral : 13.760 109.554 1061 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.16 % Allowed : 10.63 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.30), residues: 785 helix: 1.39 (0.27), residues: 396 sheet: 0.34 (0.80), residues: 45 loop : -1.33 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.007 0.001 HIS B 519 PHE 0.017 0.002 PHE A 369 TYR 0.017 0.002 TYR B 365 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7193 (t0) cc_final: 0.6990 (t0) REVERT: A 552 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7860 (mp-120) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.1877 time to fit residues: 22.3443 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6748 Z= 0.291 Angle : 0.594 7.410 9156 Z= 0.302 Chirality : 0.044 0.235 979 Planarity : 0.005 0.052 1166 Dihedral : 12.007 109.987 1060 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.87 % Allowed : 11.93 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.19 (0.30), residues: 785 helix: 1.28 (0.27), residues: 396 sheet: 0.30 (0.79), residues: 45 loop : -1.29 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.006 0.001 HIS B 519 PHE 0.016 0.002 PHE A 369 TYR 0.014 0.002 TYR A 385 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 332 MET cc_start: 0.8360 (ttm) cc_final: 0.8157 (ttt) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1691 time to fit residues: 19.3138 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6748 Z= 0.230 Angle : 0.553 8.703 9156 Z= 0.282 Chirality : 0.043 0.237 979 Planarity : 0.004 0.057 1166 Dihedral : 10.725 107.558 1060 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.01 % Allowed : 12.64 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 785 helix: 1.31 (0.27), residues: 397 sheet: 0.37 (0.79), residues: 45 loop : -1.24 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.014 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (mp) REVERT: A 332 MET cc_start: 0.8383 (ttm) cc_final: 0.8172 (ttt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.1671 time to fit residues: 18.3422 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.167 Angle : 0.509 7.866 9156 Z= 0.258 Chirality : 0.041 0.161 979 Planarity : 0.004 0.053 1166 Dihedral : 9.623 105.479 1060 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.43 (0.30), residues: 785 helix: 1.50 (0.27), residues: 384 sheet: 0.59 (0.82), residues: 44 loop : -1.14 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS B 519 PHE 0.012 0.001 PHE A 315 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.785 Fit side-chains REVERT: A 151 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 408 MET cc_start: 0.8932 (mmt) cc_final: 0.8672 (mmt) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.1753 time to fit residues: 18.9473 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6748 Z= 0.229 Angle : 0.540 8.032 9156 Z= 0.276 Chirality : 0.042 0.150 979 Planarity : 0.005 0.084 1166 Dihedral : 9.147 103.420 1056 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.72 % Allowed : 13.07 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.39 (0.30), residues: 785 helix: 1.42 (0.27), residues: 385 sheet: 0.67 (0.82), residues: 44 loop : -1.12 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.014 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.747 Fit side-chains REVERT: A 365 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 408 MET cc_start: 0.8911 (mmt) cc_final: 0.8577 (mmt) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1685 time to fit residues: 17.5720 Evaluate side-chains 74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 601 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6748 Z= 0.294 Angle : 0.575 8.535 9156 Z= 0.297 Chirality : 0.043 0.159 979 Planarity : 0.005 0.071 1166 Dihedral : 8.831 101.716 1056 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 785 helix: 1.30 (0.27), residues: 391 sheet: 0.70 (0.79), residues: 45 loop : -1.18 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.006 0.001 HIS B 519 PHE 0.016 0.002 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.737 Fit side-chains REVERT: B 375 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6110 (t80) REVERT: A 151 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8595 (mp) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.1854 time to fit residues: 18.2900 Evaluate side-chains 74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 601 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.211 Angle : 0.531 8.316 9156 Z= 0.274 Chirality : 0.041 0.152 979 Planarity : 0.005 0.066 1166 Dihedral : 8.338 100.739 1056 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.58 % Allowed : 13.65 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.32 (0.30), residues: 785 helix: 1.44 (0.27), residues: 384 sheet: 0.63 (0.80), residues: 44 loop : -1.26 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.008 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.787 Fit side-chains REVERT: B 375 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6065 (t80) REVERT: A 151 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 365 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 408 MET cc_start: 0.8906 (mmt) cc_final: 0.8610 (mmt) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1785 time to fit residues: 18.4937 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6748 Z= 0.194 Angle : 0.530 8.490 9156 Z= 0.273 Chirality : 0.041 0.149 979 Planarity : 0.005 0.063 1166 Dihedral : 7.958 98.973 1056 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.44 % Allowed : 14.51 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.30), residues: 785 helix: 1.50 (0.27), residues: 378 sheet: 0.69 (0.80), residues: 44 loop : -1.23 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 PHE 0.012 0.001 PHE A 369 TYR 0.019 0.001 TYR A 183 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.783 Fit side-chains REVERT: B 375 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6018 (t80) REVERT: A 151 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 365 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 408 MET cc_start: 0.8925 (mmt) cc_final: 0.8644 (mmt) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1818 time to fit residues: 18.7107 Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6748 Z= 0.219 Angle : 0.541 8.636 9156 Z= 0.279 Chirality : 0.041 0.149 979 Planarity : 0.005 0.084 1166 Dihedral : 7.733 97.113 1056 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.44 % Allowed : 14.80 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.30), residues: 785 helix: 1.47 (0.27), residues: 384 sheet: 0.71 (0.80), residues: 44 loop : -1.23 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 PHE 0.013 0.001 PHE A 369 TYR 0.016 0.001 TYR A 183 ARG 0.008 0.000 ARG A 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.763 Fit side-chains REVERT: B 375 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6004 (t80) REVERT: A 151 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 365 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8117 (p) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1885 time to fit residues: 19.2221 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.121396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090857 restraints weight = 11963.170| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.82 r_work: 0.3110 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.189 Angle : 0.527 8.740 9156 Z= 0.273 Chirality : 0.041 0.147 979 Planarity : 0.005 0.079 1166 Dihedral : 7.570 95.762 1056 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.44 % Allowed : 14.94 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.30), residues: 785 helix: 1.56 (0.27), residues: 377 sheet: 0.75 (0.80), residues: 44 loop : -1.15 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 PHE 0.012 0.001 PHE A 369 TYR 0.017 0.001 TYR A 183 ARG 0.008 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.20 seconds wall clock time: 32 minutes 10.01 seconds (1930.01 seconds total)