Starting phenix.real_space_refine on Sun Aug 4 22:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdz_37468/08_2024/8wdz_37468.cif" } resolution = 2.71 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= 0.026 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 6336 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 37 5.16 5 C 4195 2.51 5 N 1078 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1553 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 6.15, per 1000 atoms: 0.94 Number of scatterers: 6559 At special positions: 0 Unit cell: (76.5, 87.55, 124.1, 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 37 16.00 O 1248 8.00 N 1078 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 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 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 54.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.528A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.667A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.783A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.949A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.762A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.895A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.687A 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 220 through 249 removed outlier: 3.716A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.727A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.757A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.624A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.860A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.083A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.922A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.798A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.530A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.024A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.443A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.066A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 290 hydrogen bonds defined for protein. 821 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: 1.65 Time building geometry restraints manager: 2.71 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: 2082 1.34 - 1.46: 1737 1.46 - 1.58: 2867 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6744 Sorted by residual: bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.43e-02 4.89e+03 1.32e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.17e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.31e-02 5.83e+03 9.86e+00 bond pdb=" N HIS A 401 " pdb=" CA HIS A 401 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.66e+00 bond pdb=" N SER B 494 " pdb=" CA SER B 494 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.31e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.00: 164 106.00 - 113.02: 3504 113.02 - 120.04: 2480 120.04 - 127.07: 2924 127.07 - 134.09: 98 Bond angle restraints: 9170 Sorted by residual: angle pdb=" N GLU A 227 " pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" N LYS A 419 " pdb=" CA LYS A 419 " pdb=" C LYS A 419 " ideal model delta sigma weight residual 111.36 107.81 3.55 1.09e+00 8.42e-01 1.06e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 110.42 116.78 -6.36 1.99e+00 2.53e-01 1.02e+01 angle pdb=" C GLN A 24 " pdb=" N ALA A 25 " pdb=" CA ALA A 25 " ideal model delta sigma weight residual 120.29 124.78 -4.49 1.42e+00 4.96e-01 1.00e+01 angle pdb=" N ASN B 487 " pdb=" CA ASN B 487 " pdb=" C ASN B 487 " ideal model delta sigma weight residual 110.80 104.71 6.09 2.13e+00 2.20e-01 8.18e+00 ... (remaining 9165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 3709 17.33 - 34.66: 307 34.66 - 51.99: 68 51.99 - 69.32: 15 69.32 - 86.65: 7 Dihedral angle restraints: 4106 sinusoidal: 1780 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.81 -48.81 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 709 0.043 - 0.087: 206 0.087 - 0.130: 64 0.130 - 0.173: 6 0.173 - 0.216: 2 Chirality restraints: 987 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 984 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 486 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C VAL B 486 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 486 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " -0.017 2.00e-02 2.50e+03 1.69e-02 7.18e+00 pdb=" CG TRP A 302 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE A 400 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 400 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 401 " 0.014 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 5188 3.16 - 3.74: 9740 3.74 - 4.32: 13628 4.32 - 4.90: 22976 Nonbonded interactions: 51570 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.004 2.230 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.262 3.040 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 431 " model vdw 2.304 3.120 nonbonded pdb=" O ILE A 151 " pdb=" OG SER A 155 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASN A 90 " pdb=" N2 NAG A 902 " model vdw 2.318 3.120 ... (remaining 51565 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.004 0.052 6744 Z= 0.233 Angle : 0.592 6.364 9170 Z= 0.313 Chirality : 0.044 0.216 987 Planarity : 0.004 0.055 1176 Dihedral : 13.558 86.655 2593 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 788 helix: 1.02 (0.27), residues: 356 sheet: 1.71 (0.75), residues: 50 loop : -1.15 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 302 HIS 0.006 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.012 0.001 TYR A 183 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 483 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 549 GLU cc_start: 0.7445 (mp0) cc_final: 0.7150 (mp0) REVERT: B 438 SER cc_start: 0.8205 (t) cc_final: 0.7900 (t) outliers start: 3 outliers final: 1 residues processed: 180 average time/residue: 1.0395 time to fit residues: 197.6166 Evaluate side-chains 156 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 175 GLN A 210 ASN A 374 HIS A 394 ASN A 401 HIS A 580 ASN B 417 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6744 Z= 0.202 Angle : 0.571 9.821 9170 Z= 0.291 Chirality : 0.043 0.199 987 Planarity : 0.004 0.037 1176 Dihedral : 6.031 53.935 1070 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 11.67 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 788 helix: 1.21 (0.28), residues: 367 sheet: 0.95 (0.73), residues: 48 loop : -1.13 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.006 0.001 HIS A 241 PHE 0.017 0.001 PHE B 400 TYR 0.012 0.001 TYR A 183 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 GLU cc_start: 0.7187 (mp0) cc_final: 0.6937 (mp0) outliers start: 6 outliers final: 3 residues processed: 167 average time/residue: 1.0510 time to fit residues: 185.3146 Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 402 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 188 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 580 ASN B 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6744 Z= 0.130 Angle : 0.509 7.469 9170 Z= 0.258 Chirality : 0.041 0.190 987 Planarity : 0.003 0.031 1176 Dihedral : 5.623 53.740 1068 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 14.41 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.33 (0.31), residues: 788 helix: 1.34 (0.28), residues: 375 sheet: 0.89 (0.75), residues: 48 loop : -1.08 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.017 0.001 PHE B 400 TYR 0.010 0.001 TYR A 516 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.7008 (mp0) outliers start: 11 outliers final: 4 residues processed: 172 average time/residue: 1.0559 time to fit residues: 191.5553 Evaluate side-chains 167 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 175 GLN A 188 ASN A 210 ASN A 580 ASN B 417 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6744 Z= 0.317 Angle : 0.579 5.553 9170 Z= 0.297 Chirality : 0.046 0.245 987 Planarity : 0.004 0.035 1176 Dihedral : 5.612 54.471 1068 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.74 % Allowed : 14.99 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.14 (0.30), residues: 788 helix: 1.23 (0.28), residues: 371 sheet: 0.39 (0.81), residues: 38 loop : -1.12 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 478 HIS 0.008 0.002 HIS A 241 PHE 0.015 0.001 PHE A 308 TYR 0.015 0.002 TYR A 385 ARG 0.007 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8336 (tpp) REVERT: A 549 GLU cc_start: 0.7191 (mp0) cc_final: 0.6923 (mp0) REVERT: B 503 VAL cc_start: 0.8368 (p) cc_final: 0.8145 (t) outliers start: 19 outliers final: 6 residues processed: 167 average time/residue: 1.1014 time to fit residues: 194.0615 Evaluate side-chains 169 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 580 ASN B 417 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6744 Z= 0.183 Angle : 0.525 5.386 9170 Z= 0.266 Chirality : 0.042 0.220 987 Planarity : 0.004 0.037 1176 Dihedral : 5.284 53.409 1068 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 16.14 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.14 (0.30), residues: 788 helix: 1.30 (0.28), residues: 373 sheet: 0.25 (0.81), residues: 38 loop : -1.19 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE B 400 TYR 0.016 0.001 TYR A 454 ARG 0.008 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8508 (m) cc_final: 0.7527 (m) REVERT: A 171 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 376 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8415 (tpp) REVERT: A 549 GLU cc_start: 0.7163 (mp0) cc_final: 0.6904 (mp0) REVERT: B 355 ARG cc_start: 0.7323 (mtp85) cc_final: 0.6934 (ttt-90) REVERT: B 503 VAL cc_start: 0.8393 (p) cc_final: 0.8178 (t) outliers start: 16 outliers final: 11 residues processed: 162 average time/residue: 1.0719 time to fit residues: 183.2642 Evaluate side-chains 172 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 210 ASN A 340 GLN A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6744 Z= 0.153 Angle : 0.507 6.025 9170 Z= 0.255 Chirality : 0.041 0.204 987 Planarity : 0.004 0.032 1176 Dihedral : 5.001 53.149 1068 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.45 % Allowed : 16.86 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.28 (0.30), residues: 788 helix: 1.38 (0.27), residues: 376 sheet: 0.24 (0.80), residues: 38 loop : -1.09 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.022 0.001 TYR A 183 ARG 0.006 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8501 (m) cc_final: 0.8221 (m) REVERT: B 355 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7076 (ttt-90) REVERT: B 503 VAL cc_start: 0.8399 (p) cc_final: 0.8183 (t) outliers start: 17 outliers final: 11 residues processed: 163 average time/residue: 1.0180 time to fit residues: 175.5336 Evaluate side-chains 168 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR 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: 2.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 34 optimal weight: 0.0570 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6744 Z= 0.160 Angle : 0.520 6.283 9170 Z= 0.260 Chirality : 0.042 0.195 987 Planarity : 0.003 0.029 1176 Dihedral : 4.913 53.219 1068 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.87 % Allowed : 18.59 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.34 (0.30), residues: 788 helix: 1.41 (0.27), residues: 380 sheet: 0.19 (0.80), residues: 38 loop : -1.04 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.019 0.001 TYR A 183 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8500 (m) cc_final: 0.8223 (m) REVERT: A 359 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7886 (tt) REVERT: A 549 GLU cc_start: 0.7123 (mp0) cc_final: 0.6858 (mp0) REVERT: B 355 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7066 (ttt-90) REVERT: B 503 VAL cc_start: 0.8391 (p) cc_final: 0.8183 (t) outliers start: 13 outliers final: 8 residues processed: 165 average time/residue: 1.0177 time to fit residues: 177.5835 Evaluate side-chains 168 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6744 Z= 0.192 Angle : 0.529 7.015 9170 Z= 0.265 Chirality : 0.043 0.202 987 Planarity : 0.004 0.031 1176 Dihedral : 4.870 53.272 1068 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.87 % Allowed : 19.16 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 788 helix: 1.37 (0.27), residues: 380 sheet: 0.25 (0.81), residues: 38 loop : -1.04 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.022 0.001 TYR A 183 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8498 (m) cc_final: 0.8205 (m) REVERT: B 355 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7087 (ttt-90) REVERT: B 503 VAL cc_start: 0.8401 (p) cc_final: 0.8180 (t) outliers start: 13 outliers final: 8 residues processed: 166 average time/residue: 0.9891 time to fit residues: 173.9480 Evaluate side-chains 169 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 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 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6744 Z= 0.226 Angle : 0.557 7.526 9170 Z= 0.279 Chirality : 0.044 0.206 987 Planarity : 0.004 0.031 1176 Dihedral : 4.899 53.421 1068 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 19.31 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 788 helix: 1.34 (0.27), residues: 380 sheet: 0.23 (0.81), residues: 38 loop : -1.05 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 PHE 0.014 0.001 PHE A 327 TYR 0.017 0.001 TYR A 510 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8488 (m) cc_final: 0.8189 (m) REVERT: A 227 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: B 355 ARG cc_start: 0.7330 (mtp85) cc_final: 0.7069 (ttt-90) REVERT: B 503 VAL cc_start: 0.8397 (p) cc_final: 0.8174 (t) outliers start: 11 outliers final: 11 residues processed: 164 average time/residue: 1.0177 time to fit residues: 176.9036 Evaluate side-chains 176 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 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 175 GLN A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6744 Z= 0.202 Angle : 0.543 7.697 9170 Z= 0.270 Chirality : 0.043 0.203 987 Planarity : 0.004 0.032 1176 Dihedral : 4.843 53.271 1068 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 19.02 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 788 helix: 1.35 (0.27), residues: 380 sheet: 0.22 (0.82), residues: 38 loop : -1.06 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 PHE 0.013 0.001 PHE A 327 TYR 0.013 0.001 TYR A 613 ARG 0.002 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8490 (m) cc_final: 0.8205 (m) REVERT: A 227 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: B 503 VAL cc_start: 0.8406 (p) cc_final: 0.8180 (t) outliers start: 12 outliers final: 12 residues processed: 163 average time/residue: 1.0517 time to fit residues: 181.5016 Evaluate side-chains 173 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 25 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121737 restraints weight = 10938.697| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.29 r_work: 0.3427 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6744 Z= 0.137 Angle : 0.514 7.064 9170 Z= 0.256 Chirality : 0.041 0.203 987 Planarity : 0.003 0.029 1176 Dihedral : 4.722 53.164 1068 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.59 % Rotamer: Outliers : 1.44 % Allowed : 19.74 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.47 (0.31), residues: 788 helix: 1.56 (0.28), residues: 373 sheet: 0.24 (0.82), residues: 38 loop : -0.99 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 PHE 0.012 0.001 PHE B 400 TYR 0.012 0.001 TYR A 183 ARG 0.002 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.83 seconds wall clock time: 62 minutes 52.94 seconds (3772.94 seconds total)