Starting phenix.real_space_refine on Fri Mar 6 00:55:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204.map" model { file = "/net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7smp_25204/03_2026/7smp_25204_trim.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 83 5.16 5 C 8573 2.51 5 N 2148 2.21 5 O 2318 1.98 5 H 13353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26477 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 13184 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 29, 'TRANS': 803} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 13216 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 29, 'TRANS': 805} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' K': 1, '82U': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' K': 1, '82U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.01, per 1000 atoms: 0.19 Number of scatterers: 26477 At special positions: 0 Unit cell: (84.53, 151.94, 124.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 83 16.00 O 2318 8.00 N 2148 7.00 C 8573 6.00 H 13353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 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 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 630.7 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 65.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.524A pdb=" N TRP B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.422A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.255A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 397 removed outlier: 3.619A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 426 Processing helix chain 'B' and resid 427 through 455 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.522A pdb=" N LYS B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.727A pdb=" N GLY B 504 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 544 Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.710A pdb=" N THR B 555 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.548A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 633 removed outlier: 3.667A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 639 through 643 removed outlier: 3.681A pdb=" N LYS B 643 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 removed outlier: 3.687A pdb=" N ALA B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 699 Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 731 through 752 removed outlier: 3.625A pdb=" N LEU B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 780 removed outlier: 3.577A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 4.010A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 4.239A pdb=" N MET B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 834 " --> pdb=" O GLN B 830 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.627A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1046 through 1050 removed outlier: 3.915A pdb=" N LYS B1050 " --> pdb=" O LYS B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1119 through 1129 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.696A pdb=" N PHE A 305 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.699A pdb=" N ASN A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.648A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.659A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 4.166A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 499 Proline residue: A 496 - end of helix removed outlier: 3.576A pdb=" N THR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.421A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 Proline residue: A 519 - end of helix removed outlier: 3.526A pdb=" N SER A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.790A pdb=" N LEU A 570 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.877A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.531A pdb=" N ASP A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.706A pdb=" N ALA A 642 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 643 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 643' Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.575A pdb=" N ALA A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 699 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.861A pdb=" N ASN A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 760 through 780 Processing helix chain 'A' and resid 797 through 800 Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.060A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 849 removed outlier: 4.413A pdb=" N MET A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 889 through 893 removed outlier: 4.553A pdb=" N LEU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.666A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1136 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.774A pdb=" N SER A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.651A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 822 " --> pdb=" O ALA B 856 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 883 through 887 removed outlier: 6.596A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE B1054 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1112 through 1113 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.511A pdb=" N MET A 818 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 856 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N CYS A 820 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 858 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N HIS A 822 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A1198 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A1023 " --> pdb=" O ALA A1163 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A1165 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1112 through 1113 783 hydrogen bonds defined for protein. 2295 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: 6.01 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13337 1.03 - 1.23: 55 1.23 - 1.42: 5511 1.42 - 1.62: 7728 1.62 - 1.82: 142 Bond restraints: 26773 Sorted by residual: bond pdb=" N 82U B1302 " pdb=" CA 82U B1302 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.432 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" NE1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.34e+00 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 48435 3.70 - 7.39: 66 7.39 - 11.09: 4 11.09 - 14.78: 4 14.78 - 18.48: 8 Bond angle restraints: 48517 Sorted by residual: angle pdb=" C 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 120.11 138.59 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O1 82U B1302 " pdb=" S1 82U B1302 " pdb=" O2 82U B1302 " ideal model delta sigma weight residual 118.12 100.23 17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O1 82U A1301 " pdb=" S1 82U A1301 " pdb=" O2 82U A1301 " ideal model delta sigma weight residual 118.12 100.59 17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CD2 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 118.42 101.58 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C 82U B1302 " pdb=" C1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 120.11 136.89 -16.78 3.00e+00 1.11e-01 3.13e+01 ... (remaining 48512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11118 17.47 - 34.94: 1028 34.94 - 52.41: 262 52.41 - 69.88: 108 69.88 - 87.36: 25 Dihedral angle restraints: 12541 sinusoidal: 6757 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 34.97 58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" C 82U A1301 " pdb=" N 82U A1301 " pdb=" CA 82U A1301 " pdb=" CB 82U A1301 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" C 82U B1301 " pdb=" N 82U B1301 " pdb=" CA 82U B1301 " pdb=" CB 82U B1301 " ideal model delta harmonic sigma weight residual -122.60 -137.90 15.30 0 2.50e+00 1.60e-01 3.75e+01 ... (remaining 12538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1387 0.034 - 0.067: 512 0.067 - 0.101: 142 0.101 - 0.134: 49 0.134 - 0.168: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU B 683 " pdb=" CB LEU B 683 " pdb=" CD1 LEU B 683 " pdb=" CD2 LEU B 683 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA GLN A1149 " pdb=" N GLN A1149 " pdb=" C GLN A1149 " pdb=" CB GLN A1149 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2089 not shown) Planarity restraints: 3862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 82U B1302 " 0.073 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" CA 82U B1302 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1302 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1302 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1302 " 0.070 2.00e-02 2.50e+03 pdb=" CG 82U B1302 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 82U B1302 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1302 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1302 " -0.001 2.00e-02 2.50e+03 pdb=" S1 82U B1302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U B1301 " 0.073 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CA 82U B1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1301 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1301 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 82U B1301 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1301 " 0.000 2.00e-02 2.50e+03 pdb=" S1 82U B1301 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U A1301 " 0.072 2.00e-02 2.50e+03 8.13e-02 1.65e+02 pdb=" CA 82U A1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U A1301 " 0.079 2.00e-02 2.50e+03 pdb=" O 82U A1301 " 0.006 2.00e-02 2.50e+03 pdb=" CB 82U A1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" C1 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" C17 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" S1 82U A1301 " -0.003 2.00e-02 2.50e+03 ... (remaining 3859 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 3942 2.27 - 2.98: 73486 2.98 - 3.70: 99987 3.70 - 4.42: 151365 4.42 - 5.14: 239673 Nonbonded interactions: 568453 Sorted by model distance: nonbonded pdb=" H MET B 303 " pdb=" O4 82U B1302 " model vdw 1.548 2.450 nonbonded pdb=" O ILE B1054 " pdb=" H SER B1084 " model vdw 1.628 2.450 nonbonded pdb=" O TRP B1132 " pdb=" HG SER B1179 " model vdw 1.629 2.450 nonbonded pdb="HD22 ASN B 506 " pdb=" OG SER B 621 " model vdw 1.645 2.450 nonbonded pdb=" O GLN A 591 " pdb=" HG SER A 594 " model vdw 1.655 2.450 ... (remaining 568448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 283 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 284 through 907 or (resi \ d 908 and (name N or name CA or name C or name O or name CB or name CG or name N \ D1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1 or name HE2)) or resid 909 through 1210 or resid 130 \ 1 through 1302)) selection = (chain 'B' and (resid 283 through 1210 or resid 1302 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.590 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 0.067 13424 Z= 0.191 Angle : 0.764 18.480 18211 Z= 0.371 Chirality : 0.039 0.168 2092 Planarity : 0.006 0.082 2256 Dihedral : 14.908 87.355 4836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1660 helix: 1.17 (0.16), residues: 1017 sheet: -1.66 (0.49), residues: 114 loop : -1.84 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 348 TYR 0.022 0.001 TYR A 353 PHE 0.021 0.001 PHE B 495 TRP 0.031 0.002 TRP A 758 HIS 0.009 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00411 (13420) covalent geometry : angle 0.76346 (18203) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.08061 ( 8) hydrogen bonds : bond 0.13155 ( 783) hydrogen bonds : angle 5.71400 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1072 MET cc_start: 0.7696 (tpt) cc_final: 0.7464 (tpt) REVERT: B 1125 LYS cc_start: 0.7395 (tptt) cc_final: 0.7169 (tppt) REVERT: A 429 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 697 SER cc_start: 0.8837 (t) cc_final: 0.8255 (t) REVERT: A 713 MET cc_start: 0.7833 (ttp) cc_final: 0.7332 (ttp) REVERT: A 725 ILE cc_start: 0.8108 (mm) cc_final: 0.7888 (mm) REVERT: A 1072 MET cc_start: 0.7456 (tpt) cc_final: 0.7179 (tpt) REVERT: A 1077 SER cc_start: 0.8855 (m) cc_final: 0.8612 (m) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2308 time to fit residues: 92.0722 Evaluate side-chains 224 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 839 GLN A 398 HIS ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127716 restraints weight = 56015.887| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.37 r_work: 0.3445 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13424 Z= 0.175 Angle : 0.582 11.840 18211 Z= 0.306 Chirality : 0.039 0.129 2092 Planarity : 0.006 0.081 2256 Dihedral : 8.634 88.547 1830 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.78 % Allowed : 6.49 % Favored : 92.73 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1660 helix: 1.42 (0.16), residues: 1009 sheet: -1.79 (0.49), residues: 114 loop : -1.96 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 788 TYR 0.012 0.001 TYR A 903 PHE 0.015 0.001 PHE B 811 TRP 0.016 0.001 TRP B 287 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00383 (13420) covalent geometry : angle 0.58147 (18203) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.00413 ( 8) hydrogen bonds : bond 0.05006 ( 783) hydrogen bonds : angle 4.67316 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1072 MET cc_start: 0.7924 (tpt) cc_final: 0.7720 (tpt) REVERT: A 429 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 697 SER cc_start: 0.9025 (t) cc_final: 0.8576 (t) REVERT: A 713 MET cc_start: 0.8223 (ttp) cc_final: 0.7816 (ttp) REVERT: A 725 ILE cc_start: 0.8186 (mm) cc_final: 0.7956 (mm) outliers start: 11 outliers final: 11 residues processed: 235 average time/residue: 0.2380 time to fit residues: 84.6941 Evaluate side-chains 224 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 159 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 ASN B 731 ASN 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 = 0.156187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126943 restraints weight = 55977.986| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.37 r_work: 0.3434 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13424 Z= 0.167 Angle : 0.567 11.910 18211 Z= 0.296 Chirality : 0.039 0.170 2092 Planarity : 0.005 0.081 2256 Dihedral : 8.254 89.265 1830 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.43 % Allowed : 8.62 % Favored : 89.95 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1660 helix: 1.45 (0.16), residues: 1011 sheet: -1.74 (0.50), residues: 110 loop : -1.96 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.012 0.001 TYR A 903 PHE 0.014 0.001 PHE B 811 TRP 0.017 0.001 TRP B 732 HIS 0.004 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00371 (13420) covalent geometry : angle 0.56677 (18203) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.18425 ( 8) hydrogen bonds : bond 0.04582 ( 783) hydrogen bonds : angle 4.50802 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.661 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: B 363 GLU cc_start: 0.8800 (pm20) cc_final: 0.8595 (pm20) REVERT: B 468 TYR cc_start: 0.7381 (m-80) cc_final: 0.6859 (m-80) REVERT: B 1072 MET cc_start: 0.7990 (tpt) cc_final: 0.7668 (tpt) REVERT: A 429 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 697 SER cc_start: 0.9004 (t) cc_final: 0.8451 (t) REVERT: A 713 MET cc_start: 0.8147 (ttp) cc_final: 0.7725 (ttp) REVERT: A 725 ILE cc_start: 0.8244 (mm) cc_final: 0.8011 (mm) outliers start: 20 outliers final: 16 residues processed: 248 average time/residue: 0.2218 time to fit residues: 83.3094 Evaluate side-chains 239 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 0.0060 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN B 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129237 restraints weight = 55218.292| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.34 r_work: 0.3464 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13424 Z= 0.116 Angle : 0.533 11.006 18211 Z= 0.275 Chirality : 0.038 0.224 2092 Planarity : 0.005 0.081 2256 Dihedral : 7.732 84.911 1830 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.14 % Allowed : 9.84 % Favored : 89.02 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1660 helix: 1.64 (0.16), residues: 1011 sheet: -1.63 (0.51), residues: 108 loop : -1.94 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1151 TYR 0.014 0.001 TYR A 353 PHE 0.013 0.001 PHE B 811 TRP 0.022 0.001 TRP B 732 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00251 (13420) covalent geometry : angle 0.53253 (18203) SS BOND : bond 0.00437 ( 4) SS BOND : angle 1.20960 ( 8) hydrogen bonds : bond 0.04193 ( 783) hydrogen bonds : angle 4.29982 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.607 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: symmetry clash revert: symmetry clash REVERT: B 731 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7520 (t0) REVERT: B 1050 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6751 (mtpt) REVERT: B 1072 MET cc_start: 0.7891 (tpt) cc_final: 0.7518 (tpt) REVERT: A 429 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 697 SER cc_start: 0.9016 (t) cc_final: 0.8490 (t) REVERT: A 713 MET cc_start: 0.8091 (ttp) cc_final: 0.7679 (ttp) REVERT: A 725 ILE cc_start: 0.8162 (mm) cc_final: 0.7903 (mm) REVERT: A 805 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8821 (mp) outliers start: 16 outliers final: 11 residues processed: 246 average time/residue: 0.2306 time to fit residues: 86.1575 Evaluate side-chains 238 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124752 restraints weight = 56145.737| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.36 r_work: 0.3408 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13424 Z= 0.217 Angle : 0.592 12.060 18211 Z= 0.311 Chirality : 0.040 0.196 2092 Planarity : 0.005 0.081 2256 Dihedral : 7.492 83.652 1830 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.57 % Allowed : 10.69 % Favored : 87.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1660 helix: 1.49 (0.16), residues: 1012 sheet: -1.80 (0.51), residues: 108 loop : -2.00 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 788 TYR 0.013 0.001 TYR A 903 PHE 0.020 0.001 PHE A1210 TRP 0.023 0.002 TRP B 732 HIS 0.004 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00490 (13420) covalent geometry : angle 0.59161 (18203) SS BOND : bond 0.00540 ( 4) SS BOND : angle 1.13036 ( 8) hydrogen bonds : bond 0.04513 ( 783) hydrogen bonds : angle 4.44896 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.668 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: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.7519 (m-80) cc_final: 0.7111 (m-80) REVERT: B 1050 LYS cc_start: 0.7252 (mmtt) cc_final: 0.6768 (mtpt) REVERT: B 1072 MET cc_start: 0.7934 (tpt) cc_final: 0.7617 (tpt) REVERT: A 429 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 725 ILE cc_start: 0.8227 (mm) cc_final: 0.7987 (mm) REVERT: A 805 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8841 (mp) outliers start: 22 outliers final: 19 residues processed: 236 average time/residue: 0.2310 time to fit residues: 82.1274 Evaluate side-chains 240 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 0.0070 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127796 restraints weight = 55392.226| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.32 r_work: 0.3448 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13424 Z= 0.124 Angle : 0.541 11.183 18211 Z= 0.279 Chirality : 0.038 0.179 2092 Planarity : 0.005 0.081 2256 Dihedral : 6.872 78.674 1830 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.64 % Allowed : 11.40 % Favored : 86.96 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1660 helix: 1.63 (0.16), residues: 1016 sheet: -1.72 (0.50), residues: 108 loop : -1.92 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1151 TYR 0.015 0.001 TYR A 353 PHE 0.013 0.001 PHE B 811 TRP 0.021 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00270 (13420) covalent geometry : angle 0.54063 (18203) SS BOND : bond 0.00418 ( 4) SS BOND : angle 1.07919 ( 8) hydrogen bonds : bond 0.04190 ( 783) hydrogen bonds : angle 4.28225 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.671 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: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.7550 (m-80) cc_final: 0.7039 (m-80) REVERT: B 1072 MET cc_start: 0.7931 (tpt) cc_final: 0.7570 (tpt) REVERT: A 429 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 697 SER cc_start: 0.8971 (t) cc_final: 0.8610 (t) REVERT: A 713 MET cc_start: 0.8312 (ttp) cc_final: 0.7930 (ttp) REVERT: A 725 ILE cc_start: 0.8211 (mm) cc_final: 0.7970 (mm) REVERT: A 805 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8840 (mp) outliers start: 23 outliers final: 21 residues processed: 242 average time/residue: 0.2392 time to fit residues: 86.9662 Evaluate side-chains 245 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1128 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126803 restraints weight = 55700.104| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.33 r_work: 0.3434 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13424 Z= 0.148 Angle : 0.550 11.301 18211 Z= 0.286 Chirality : 0.038 0.141 2092 Planarity : 0.005 0.080 2256 Dihedral : 6.313 72.316 1830 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.78 % Allowed : 11.69 % Favored : 86.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1660 helix: 1.65 (0.16), residues: 1012 sheet: -1.81 (0.50), residues: 108 loop : -1.97 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1201 TYR 0.017 0.001 TYR A 353 PHE 0.014 0.001 PHE B 811 TRP 0.031 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00332 (13420) covalent geometry : angle 0.55006 (18203) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.11514 ( 8) hydrogen bonds : bond 0.04207 ( 783) hydrogen bonds : angle 4.27443 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.643 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: symmetry clash REVERT: B 468 TYR cc_start: 0.7651 (m-80) cc_final: 0.7235 (m-80) REVERT: B 589 ASN cc_start: 0.7848 (t0) cc_final: 0.7360 (t0) REVERT: B 1072 MET cc_start: 0.7955 (tpt) cc_final: 0.7629 (tpt) REVERT: A 429 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 697 SER cc_start: 0.9019 (t) cc_final: 0.8689 (t) REVERT: A 713 MET cc_start: 0.8249 (ttp) cc_final: 0.7938 (ttp) REVERT: A 725 ILE cc_start: 0.8096 (mm) cc_final: 0.7864 (mm) REVERT: A 805 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8818 (mp) outliers start: 25 outliers final: 22 residues processed: 243 average time/residue: 0.2357 time to fit residues: 85.8467 Evaluate side-chains 249 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1128 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126900 restraints weight = 55617.409| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.31 r_work: 0.3433 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13424 Z= 0.147 Angle : 0.547 11.193 18211 Z= 0.283 Chirality : 0.038 0.125 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.742 60.787 1830 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.71 % Allowed : 12.33 % Favored : 85.96 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1660 helix: 1.66 (0.16), residues: 1012 sheet: -1.79 (0.50), residues: 108 loop : -1.95 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1201 TYR 0.017 0.001 TYR A 353 PHE 0.014 0.001 PHE B 811 TRP 0.029 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00329 (13420) covalent geometry : angle 0.54673 (18203) SS BOND : bond 0.00427 ( 4) SS BOND : angle 1.12267 ( 8) hydrogen bonds : bond 0.04187 ( 783) hydrogen bonds : angle 4.24248 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.589 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: symmetry clash REVERT: B 468 TYR cc_start: 0.7726 (m-80) cc_final: 0.7318 (m-80) REVERT: B 589 ASN cc_start: 0.7830 (t0) cc_final: 0.7316 (t0) REVERT: B 1072 MET cc_start: 0.7968 (tpt) cc_final: 0.7651 (tpt) REVERT: A 429 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 697 SER cc_start: 0.9014 (t) cc_final: 0.8689 (t) REVERT: A 713 MET cc_start: 0.8231 (ttp) cc_final: 0.7963 (mtp) REVERT: A 725 ILE cc_start: 0.8110 (mm) cc_final: 0.7883 (mm) REVERT: A 805 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8836 (mp) outliers start: 24 outliers final: 21 residues processed: 246 average time/residue: 0.2300 time to fit residues: 85.4519 Evaluate side-chains 251 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1128 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126967 restraints weight = 55637.216| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.31 r_work: 0.3436 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13424 Z= 0.145 Angle : 0.549 11.251 18211 Z= 0.284 Chirality : 0.039 0.198 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.319 59.916 1830 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.64 % Allowed : 12.69 % Favored : 85.67 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1660 helix: 1.66 (0.16), residues: 1017 sheet: -1.80 (0.50), residues: 108 loop : -1.92 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1201 TYR 0.017 0.001 TYR A 353 PHE 0.014 0.001 PHE B 811 TRP 0.033 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00325 (13420) covalent geometry : angle 0.54899 (18203) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.13979 ( 8) hydrogen bonds : bond 0.04175 ( 783) hydrogen bonds : angle 4.23343 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.653 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: B 468 TYR cc_start: 0.7719 (m-80) cc_final: 0.7368 (m-80) REVERT: B 589 ASN cc_start: 0.7804 (t0) cc_final: 0.7304 (t0) REVERT: B 1072 MET cc_start: 0.7986 (tpt) cc_final: 0.7673 (tpt) REVERT: A 429 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 697 SER cc_start: 0.9030 (t) cc_final: 0.8683 (t) REVERT: A 713 MET cc_start: 0.8248 (ttp) cc_final: 0.7935 (ttp) REVERT: A 725 ILE cc_start: 0.8111 (mm) cc_final: 0.7896 (mm) REVERT: A 805 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 1118 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7364 (ptmt) outliers start: 23 outliers final: 17 residues processed: 242 average time/residue: 0.2408 time to fit residues: 87.4482 Evaluate side-chains 246 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126669 restraints weight = 55580.967| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.31 r_work: 0.3432 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13424 Z= 0.149 Angle : 0.549 11.208 18211 Z= 0.285 Chirality : 0.039 0.149 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.946 59.260 1830 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.35 % Allowed : 13.19 % Favored : 85.46 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1660 helix: 1.66 (0.16), residues: 1018 sheet: -1.81 (0.50), residues: 108 loop : -1.92 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1201 TYR 0.018 0.001 TYR A 353 PHE 0.015 0.001 PHE B 473 TRP 0.034 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00333 (13420) covalent geometry : angle 0.54880 (18203) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.13669 ( 8) hydrogen bonds : bond 0.04180 ( 783) hydrogen bonds : angle 4.21807 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.641 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: symmetry clash REVERT: B 468 TYR cc_start: 0.7749 (m-80) cc_final: 0.7418 (m-80) REVERT: B 589 ASN cc_start: 0.7833 (t0) cc_final: 0.7278 (t0) REVERT: B 851 MET cc_start: 0.8870 (tpp) cc_final: 0.8629 (tpp) REVERT: B 1072 MET cc_start: 0.8063 (tpt) cc_final: 0.7753 (tpt) REVERT: A 429 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 697 SER cc_start: 0.9029 (t) cc_final: 0.8666 (t) REVERT: A 713 MET cc_start: 0.8251 (ttp) cc_final: 0.7948 (ttp) REVERT: A 725 ILE cc_start: 0.8107 (mm) cc_final: 0.7892 (mm) REVERT: A 805 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (mp) REVERT: A 1118 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7347 (ptmt) outliers start: 19 outliers final: 17 residues processed: 242 average time/residue: 0.2402 time to fit residues: 86.9676 Evaluate side-chains 246 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 164 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128487 restraints weight = 55295.592| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.31 r_work: 0.3455 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13424 Z= 0.117 Angle : 0.533 11.117 18211 Z= 0.274 Chirality : 0.038 0.137 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.775 58.881 1830 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.07 % Allowed : 13.47 % Favored : 85.46 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1660 helix: 1.76 (0.16), residues: 1019 sheet: -1.76 (0.50), residues: 108 loop : -1.87 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 844 TYR 0.019 0.001 TYR A 353 PHE 0.012 0.001 PHE B 811 TRP 0.041 0.001 TRP B 732 HIS 0.002 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00257 (13420) covalent geometry : angle 0.53249 (18203) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.12902 ( 8) hydrogen bonds : bond 0.03997 ( 783) hydrogen bonds : angle 4.13148 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6581.25 seconds wall clock time: 112 minutes 3.54 seconds (6723.54 seconds total)