Starting phenix.real_space_refine on Sat Nov 16 07:39:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iu1_60886/11_2024/9iu1_60886.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 4904 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4222 2.51 5 N 1076 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6603 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1557 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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: 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: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "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 Time building chain proxies: 5.28, per 1000 atoms: 0.80 Number of scatterers: 6603 At special positions: 0 Unit cell: (87.435, 86.43, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1268 8.00 N 1076 7.00 C 4222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " 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 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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 524 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG B1300 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 903.4 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 52.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.697A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.822A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 157 through 174 removed outlier: 4.598A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.791A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (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 221 through 249 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.814A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 283 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.734A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.859A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.602A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 removed outlier: 4.283A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 4.049A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 485 removed outlier: 4.463A pdb=" N MET A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.544A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.990A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.266A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.299A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.780A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.839A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.640A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 432 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 281 hydrogen bonds defined for protein. 810 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: 1.69 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2077 1.34 - 1.46: 1507 1.46 - 1.58: 3149 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6791 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.570 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 8859 1.31 - 2.61: 285 2.61 - 3.92: 54 3.92 - 5.23: 22 5.23 - 6.53: 10 Bond angle restraints: 9230 Sorted by residual: angle pdb=" C ASN B 417 " pdb=" N ILE B 418 " pdb=" CA ILE B 418 " ideal model delta sigma weight residual 120.60 124.24 -3.64 1.29e+00 6.01e-01 7.97e+00 angle pdb=" N THR B 522 " pdb=" CA THR B 522 " pdb=" C THR B 522 " ideal model delta sigma weight residual 110.80 116.40 -5.60 2.13e+00 2.20e-01 6.90e+00 angle pdb=" CA ILE A 468 " pdb=" C ILE A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 116.57 118.99 -2.42 9.80e-01 1.04e+00 6.12e+00 angle pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" C LEU A 450 " ideal model delta sigma weight residual 109.81 114.92 -5.11 2.21e+00 2.05e-01 5.34e+00 angle pdb=" C ASP B 420 " pdb=" N TYR B 421 " pdb=" CA TYR B 421 " ideal model delta sigma weight residual 121.98 118.71 3.27 1.53e+00 4.27e-01 4.57e+00 ... (remaining 9225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 3782 22.08 - 44.17: 317 44.17 - 66.25: 47 66.25 - 88.34: 22 88.34 - 110.42: 10 Dihedral angle restraints: 4178 sinusoidal: 1857 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -161.61 75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 524 " pdb=" CB CYS B 524 " ideal model delta sinusoidal sigma weight residual 93.00 138.37 -45.37 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ALA B 521 " pdb=" C ALA B 521 " pdb=" N THR B 522 " pdb=" CA THR B 522 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 4175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 863 0.061 - 0.121: 125 0.121 - 0.182: 11 0.182 - 0.242: 1 0.242 - 0.303: 3 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 546 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1000 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 199 " 0.014 2.00e-02 2.50e+03 1.51e-02 4.57e+00 pdb=" CG TYR A 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 199 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 199 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 199 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 199 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 199 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 199 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " -0.013 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP A 477 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO A 415 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.021 5.00e-02 4.00e+02 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1303 2.77 - 3.30: 6581 3.30 - 3.84: 11079 3.84 - 4.37: 11746 4.37 - 4.90: 19875 Nonbonded interactions: 50584 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" OD1 ASN B 394 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 356 " pdb=" O ALA B 397 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 411 " pdb=" OE1 GLN A 526 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 482 " pdb=" O THR A 608 " model vdw 2.303 3.120 ... (remaining 50579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.640 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 0.044 6791 Z= 0.207 Angle : 0.600 6.532 9230 Z= 0.293 Chirality : 0.045 0.303 1003 Planarity : 0.003 0.037 1173 Dihedral : 17.138 110.421 2670 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.02 (0.31), residues: 786 helix: 1.93 (0.29), residues: 361 sheet: 2.25 (1.21), residues: 22 loop : -2.08 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE A 523 TYR 0.034 0.001 TYR A 199 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8630 (m) cc_final: 0.7949 (t) REVERT: A 72 PHE cc_start: 0.8554 (t80) cc_final: 0.8227 (t80) REVERT: A 83 TYR cc_start: 0.6487 (m-80) cc_final: 0.4803 (m-80) REVERT: A 189 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8306 (mm-30) REVERT: A 207 TYR cc_start: 0.7867 (m-80) cc_final: 0.7536 (m-80) REVERT: A 232 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 279 TYR cc_start: 0.7245 (t80) cc_final: 0.6961 (t80) REVERT: A 483 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 518 ARG cc_start: 0.6955 (ppt170) cc_final: 0.6304 (ppt170) REVERT: A 557 MET cc_start: 0.8294 (tmm) cc_final: 0.8035 (ppp) REVERT: B 347 PHE cc_start: 0.6552 (m-10) cc_final: 0.4919 (m-80) REVERT: B 351 TYR cc_start: 0.6728 (t80) cc_final: 0.6407 (t80) REVERT: B 353 TRP cc_start: 0.7597 (p-90) cc_final: 0.7029 (p-90) REVERT: B 355 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7360 (mmm-85) REVERT: B 442 ASP cc_start: 0.7889 (t70) cc_final: 0.7041 (p0) REVERT: B 444 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7875 (mmtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1989 time to fit residues: 47.7963 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6791 Z= 0.292 Angle : 0.680 8.289 9230 Z= 0.350 Chirality : 0.047 0.269 1003 Planarity : 0.005 0.044 1173 Dihedral : 11.337 72.677 1143 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % 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: -0.45 (0.31), residues: 786 helix: 1.41 (0.28), residues: 371 sheet: 0.04 (0.89), residues: 32 loop : -2.21 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 461 HIS 0.009 0.002 HIS A 228 PHE 0.019 0.002 PHE B 464 TYR 0.023 0.002 TYR B 453 ARG 0.003 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8469 (m) cc_final: 0.7542 (t) REVERT: A 72 PHE cc_start: 0.8502 (t80) cc_final: 0.8168 (t80) REVERT: A 207 TYR cc_start: 0.7964 (m-80) cc_final: 0.7669 (m-80) REVERT: A 265 HIS cc_start: 0.7809 (p90) cc_final: 0.7215 (p90) REVERT: A 474 MET cc_start: 0.8106 (mmm) cc_final: 0.7856 (mmm) REVERT: A 483 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 351 TYR cc_start: 0.7097 (t80) cc_final: 0.6596 (t80) REVERT: B 353 TRP cc_start: 0.7674 (p-90) cc_final: 0.6729 (p-90) REVERT: B 442 ASP cc_start: 0.8040 (t70) cc_final: 0.7168 (p0) REVERT: B 444 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7885 (mmtt) REVERT: B 457 ARG cc_start: 0.7846 (tmt-80) cc_final: 0.7158 (tmt-80) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1943 time to fit residues: 36.7301 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 53 optimal weight: 0.0770 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6791 Z= 0.172 Angle : 0.611 12.225 9230 Z= 0.307 Chirality : 0.044 0.263 1003 Planarity : 0.004 0.042 1173 Dihedral : 9.794 63.637 1143 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -0.31 (0.31), residues: 786 helix: 1.49 (0.28), residues: 372 sheet: 0.18 (0.94), residues: 32 loop : -2.09 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.004 0.001 HIS A 535 PHE 0.020 0.001 PHE B 464 TYR 0.019 0.001 TYR B 453 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8442 (m) cc_final: 0.7525 (t) REVERT: A 72 PHE cc_start: 0.8354 (t80) cc_final: 0.8044 (t80) REVERT: A 82 MET cc_start: 0.7803 (ptp) cc_final: 0.7596 (ptt) REVERT: A 83 TYR cc_start: 0.6354 (m-80) cc_final: 0.5627 (m-80) REVERT: A 207 TYR cc_start: 0.7817 (m-80) cc_final: 0.7575 (m-80) REVERT: A 232 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7979 (mt-10) REVERT: A 418 LEU cc_start: 0.8931 (mm) cc_final: 0.8601 (tp) REVERT: A 483 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7285 (mt-10) REVERT: B 351 TYR cc_start: 0.6886 (t80) cc_final: 0.6427 (t80) REVERT: B 353 TRP cc_start: 0.7692 (p-90) cc_final: 0.7458 (p-90) REVERT: B 355 ARG cc_start: 0.7993 (tpp80) cc_final: 0.6652 (mmm-85) REVERT: B 387 LEU cc_start: 0.8797 (tp) cc_final: 0.8594 (tp) REVERT: B 405 ASN cc_start: 0.7012 (p0) cc_final: 0.6695 (p0) REVERT: B 409 GLN cc_start: 0.7439 (mm-40) cc_final: 0.6951 (mt0) REVERT: B 423 TYR cc_start: 0.7512 (t80) cc_final: 0.7045 (t80) REVERT: B 442 ASP cc_start: 0.7444 (t70) cc_final: 0.7084 (p0) REVERT: B 444 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7890 (mmtt) REVERT: B 457 ARG cc_start: 0.7566 (tmt-80) cc_final: 0.6901 (tmt-80) REVERT: B 494 TYR cc_start: 0.6289 (m-80) cc_final: 0.5996 (m-80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1919 time to fit residues: 38.1664 Evaluate side-chains 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6791 Z= 0.162 Angle : 0.612 10.340 9230 Z= 0.308 Chirality : 0.045 0.262 1003 Planarity : 0.005 0.091 1173 Dihedral : 8.577 56.054 1143 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -0.35 (0.31), residues: 786 helix: 1.45 (0.28), residues: 372 sheet: 0.13 (0.93), residues: 32 loop : -2.11 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.010 0.001 HIS A 228 PHE 0.016 0.001 PHE A 512 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8485 (m) cc_final: 0.7629 (t) REVERT: A 72 PHE cc_start: 0.8609 (t80) cc_final: 0.8180 (t80) REVERT: A 181 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 189 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8278 (mm-30) REVERT: A 355 ASP cc_start: 0.8292 (t0) cc_final: 0.7484 (p0) REVERT: A 406 GLU cc_start: 0.6216 (mt-10) cc_final: 0.6007 (mt-10) REVERT: A 418 LEU cc_start: 0.8833 (mm) cc_final: 0.8517 (tp) REVERT: A 483 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 589 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7530 (mt-10) REVERT: B 351 TYR cc_start: 0.7117 (t80) cc_final: 0.6791 (t80) REVERT: B 423 TYR cc_start: 0.7555 (t80) cc_final: 0.7254 (t80) REVERT: B 442 ASP cc_start: 0.7672 (t70) cc_final: 0.7168 (p0) REVERT: B 444 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7939 (mmtt) REVERT: B 457 ARG cc_start: 0.7515 (tmt-80) cc_final: 0.7171 (tmt-80) REVERT: B 494 TYR cc_start: 0.6188 (m-80) cc_final: 0.5929 (m-80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1720 time to fit residues: 34.3120 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6791 Z= 0.170 Angle : 0.614 8.621 9230 Z= 0.314 Chirality : 0.044 0.268 1003 Planarity : 0.004 0.039 1173 Dihedral : 8.123 58.114 1143 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.36 (0.31), residues: 786 helix: 1.47 (0.28), residues: 372 sheet: 0.11 (0.93), residues: 32 loop : -2.15 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 477 HIS 0.008 0.001 HIS A 228 PHE 0.026 0.002 PHE A 400 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8448 (m) cc_final: 0.7679 (t) REVERT: A 72 PHE cc_start: 0.8588 (t80) cc_final: 0.8139 (t80) REVERT: A 181 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 418 LEU cc_start: 0.8859 (mm) cc_final: 0.8502 (tp) REVERT: A 477 TRP cc_start: 0.7792 (t-100) cc_final: 0.6740 (t-100) REVERT: A 589 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7589 (mt-10) REVERT: B 351 TYR cc_start: 0.7050 (t80) cc_final: 0.6592 (t80) REVERT: B 442 ASP cc_start: 0.7740 (t70) cc_final: 0.7257 (p0) REVERT: B 444 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7899 (mmtt) REVERT: B 457 ARG cc_start: 0.7621 (tmt-80) cc_final: 0.7327 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1799 time to fit residues: 34.2529 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6791 Z= 0.169 Angle : 0.595 7.571 9230 Z= 0.308 Chirality : 0.043 0.271 1003 Planarity : 0.004 0.039 1173 Dihedral : 7.340 47.869 1143 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -0.36 (0.31), residues: 786 helix: 1.44 (0.28), residues: 372 sheet: 0.29 (0.90), residues: 32 loop : -2.13 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 477 HIS 0.010 0.001 HIS A 239 PHE 0.017 0.001 PHE A 592 TYR 0.017 0.001 TYR B 453 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8474 (m) cc_final: 0.7721 (t) REVERT: A 72 PHE cc_start: 0.8560 (t80) cc_final: 0.8130 (t80) REVERT: A 181 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7789 (mp0) REVERT: A 418 LEU cc_start: 0.8881 (mm) cc_final: 0.8513 (tp) REVERT: A 477 TRP cc_start: 0.7796 (t-100) cc_final: 0.6594 (t-100) REVERT: A 589 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7563 (mt-10) REVERT: A 592 PHE cc_start: 0.7892 (t80) cc_final: 0.7687 (t80) REVERT: B 351 TYR cc_start: 0.7112 (t80) cc_final: 0.6694 (t80) REVERT: B 442 ASP cc_start: 0.7656 (t70) cc_final: 0.7237 (p0) REVERT: B 444 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7897 (mmtt) REVERT: B 457 ARG cc_start: 0.7562 (tmt-80) cc_final: 0.7337 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1806 time to fit residues: 34.2847 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 0.0570 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6791 Z= 0.151 Angle : 0.594 6.887 9230 Z= 0.305 Chirality : 0.043 0.276 1003 Planarity : 0.004 0.039 1173 Dihedral : 6.803 48.502 1143 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.27 (0.31), residues: 786 helix: 1.48 (0.28), residues: 369 sheet: 0.51 (0.91), residues: 32 loop : -2.04 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 477 HIS 0.009 0.001 HIS A 239 PHE 0.014 0.001 PHE B 464 TYR 0.020 0.001 TYR B 453 ARG 0.006 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8416 (m) cc_final: 0.7774 (t) REVERT: A 72 PHE cc_start: 0.8528 (t80) cc_final: 0.8120 (t80) REVERT: A 181 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7881 (mp0) REVERT: A 222 LEU cc_start: 0.9233 (mt) cc_final: 0.9025 (mt) REVERT: A 418 LEU cc_start: 0.8840 (mm) cc_final: 0.8525 (tp) REVERT: A 589 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7552 (mt-10) REVERT: A 592 PHE cc_start: 0.7849 (t80) cc_final: 0.7649 (t80) REVERT: B 351 TYR cc_start: 0.7103 (t80) cc_final: 0.6696 (t80) REVERT: B 442 ASP cc_start: 0.7714 (t70) cc_final: 0.7449 (p0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1853 time to fit residues: 33.4475 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.0000 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6791 Z= 0.165 Angle : 0.603 7.353 9230 Z= 0.308 Chirality : 0.043 0.276 1003 Planarity : 0.004 0.041 1173 Dihedral : 6.534 48.038 1143 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.40 (0.30), residues: 786 helix: 1.38 (0.28), residues: 369 sheet: 0.58 (0.90), residues: 32 loop : -2.12 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 477 HIS 0.009 0.001 HIS A 239 PHE 0.013 0.001 PHE A 512 TYR 0.022 0.001 TYR B 453 ARG 0.005 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8445 (m) cc_final: 0.7782 (t) REVERT: A 181 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7815 (mp0) REVERT: A 222 LEU cc_start: 0.9197 (mt) cc_final: 0.8996 (mt) REVERT: A 418 LEU cc_start: 0.8835 (mm) cc_final: 0.8495 (tp) REVERT: A 455 MET cc_start: 0.8270 (mmt) cc_final: 0.7881 (mmm) REVERT: A 589 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7543 (mt-10) REVERT: A 592 PHE cc_start: 0.7926 (t80) cc_final: 0.7715 (t80) REVERT: A 594 TRP cc_start: 0.7815 (t-100) cc_final: 0.7361 (t60) REVERT: B 351 TYR cc_start: 0.7128 (t80) cc_final: 0.6746 (t80) REVERT: B 442 ASP cc_start: 0.7746 (t70) cc_final: 0.7164 (p0) REVERT: B 444 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7900 (mmtt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1807 time to fit residues: 32.2137 Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6791 Z= 0.148 Angle : 0.602 6.812 9230 Z= 0.306 Chirality : 0.043 0.279 1003 Planarity : 0.004 0.041 1173 Dihedral : 6.199 48.274 1143 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.41 (0.30), residues: 786 helix: 1.38 (0.28), residues: 364 sheet: 0.61 (0.92), residues: 32 loop : -2.09 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 477 HIS 0.012 0.001 HIS A 239 PHE 0.012 0.001 PHE A 32 TYR 0.023 0.001 TYR B 453 ARG 0.005 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8376 (m) cc_final: 0.7752 (t) REVERT: A 72 PHE cc_start: 0.8599 (t80) cc_final: 0.8258 (t80) REVERT: A 181 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 418 LEU cc_start: 0.8756 (mm) cc_final: 0.8481 (tp) REVERT: A 455 MET cc_start: 0.8180 (mmt) cc_final: 0.7792 (mmm) REVERT: A 589 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7637 (mt-10) REVERT: A 592 PHE cc_start: 0.7883 (t80) cc_final: 0.7676 (t80) REVERT: B 351 TYR cc_start: 0.7106 (t80) cc_final: 0.6688 (t80) REVERT: B 357 ARG cc_start: 0.7558 (tmm-80) cc_final: 0.7123 (tmm-80) REVERT: B 442 ASP cc_start: 0.7722 (t70) cc_final: 0.7158 (p0) REVERT: B 444 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7858 (mmtt) REVERT: B 457 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7416 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2030 time to fit residues: 37.5188 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6791 Z= 0.174 Angle : 0.616 7.430 9230 Z= 0.314 Chirality : 0.044 0.278 1003 Planarity : 0.004 0.043 1173 Dihedral : 6.230 47.434 1143 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.43 (0.30), residues: 786 helix: 1.40 (0.28), residues: 364 sheet: 0.52 (0.91), residues: 32 loop : -2.13 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 477 HIS 0.009 0.002 HIS A 239 PHE 0.012 0.001 PHE B 464 TYR 0.030 0.002 TYR B 449 ARG 0.005 0.000 ARG B 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8261 (m) cc_final: 0.7528 (t) REVERT: A 72 PHE cc_start: 0.8630 (t80) cc_final: 0.8296 (t80) REVERT: A 181 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 418 LEU cc_start: 0.8783 (mm) cc_final: 0.8504 (tp) REVERT: A 455 MET cc_start: 0.8210 (mmt) cc_final: 0.7861 (mmm) REVERT: A 589 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7539 (mt-10) REVERT: A 592 PHE cc_start: 0.7861 (t80) cc_final: 0.7651 (t80) REVERT: B 351 TYR cc_start: 0.7142 (t80) cc_final: 0.6700 (t80) REVERT: B 442 ASP cc_start: 0.7841 (t70) cc_final: 0.7203 (p0) REVERT: B 444 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7857 (mmtt) REVERT: B 457 ARG cc_start: 0.7611 (tmt-80) cc_final: 0.6836 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1794 time to fit residues: 32.3524 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132437 restraints weight = 18675.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136376 restraints weight = 13066.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137329 restraints weight = 8354.912| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6791 Z= 0.169 Angle : 0.617 7.438 9230 Z= 0.314 Chirality : 0.044 0.280 1003 Planarity : 0.004 0.041 1173 Dihedral : 6.209 48.781 1143 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.37 (0.31), residues: 786 helix: 1.46 (0.28), residues: 363 sheet: 0.50 (0.91), residues: 32 loop : -2.11 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 477 HIS 0.009 0.001 HIS A 239 PHE 0.018 0.001 PHE B 392 TYR 0.022 0.002 TYR B 453 ARG 0.005 0.000 ARG B 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.95 seconds wall clock time: 34 minutes 0.86 seconds (2040.86 seconds total)