Starting phenix.real_space_refine on Fri Oct 23 09:53:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibc_52808/10_2026/9ibc_52808.map" } resolution = 3.51 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 C 5752 2.51 5 N 1624 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9198 Number of models: 1 Model: "" Number of chains: 5 Chain: "LF" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2224 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 3 Chain: "LV" Number of atoms: 6304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6304 Classifications: {'peptide': 807} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 38, 'TRANS': 768} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "LZ" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 199 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 39} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'HIS:plan': 2, 'GLU:plan': 4, 'PHE:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "TN" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 4, 'TRANS': 39} Chain: "RN" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 1.59, per 1000 atoms: 0.17 Number of scatterers: 9198 At special positions: 0 Unit cell: (112.89, 106.5, 119.28, 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) S 54 16.00 P 6 15.00 O 1762 8.00 N 1624 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.79 Conformation dependent library (CDL) restraints added in 305.4 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 61.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'LF' and resid 13 through 45 removed outlier: 4.305A pdb=" N ALALF 21 " --> pdb=" O GLULF 17 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEULF 22 " --> pdb=" O ALALF 18 " (cutoff:3.500A) Processing helix chain 'LF' and resid 54 through 65 Processing helix chain 'LF' and resid 66 through 79 removed outlier: 3.654A pdb=" N VALLF 70 " --> pdb=" O LYSLF 66 " (cutoff:3.500A) Processing helix chain 'LF' and resid 90 through 101 removed outlier: 4.036A pdb=" N VALLF 99 " --> pdb=" O ALALF 95 " (cutoff:3.500A) Processing helix chain 'LF' and resid 103 through 108 removed outlier: 3.518A pdb=" N LEULF 107 " --> pdb=" O ILELF 103 " (cutoff:3.500A) Processing helix chain 'LF' and resid 118 through 130 Processing helix chain 'LF' and resid 131 through 162 Processing helix chain 'LF' and resid 226 through 236 Processing helix chain 'LF' and resid 236 through 252 Processing helix chain 'LF' and resid 262 through 277 Processing helix chain 'LF' and resid 379 through 391 Processing helix chain 'LF' and resid 426 through 432 Processing helix chain 'LF' and resid 436 through 464 removed outlier: 3.588A pdb=" N TYRLF 440 " --> pdb=" O SERLF 436 " (cutoff:3.500A) Processing helix chain 'LF' and resid 471 through 488 Processing helix chain 'LV' and resid 162 through 174 Processing helix chain 'LV' and resid 187 through 195 removed outlier: 3.552A pdb=" N ASNLV 193 " --> pdb=" O VALLV 189 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALALV 194 " --> pdb=" O GLULV 190 " (cutoff:3.500A) Processing helix chain 'LV' and resid 198 through 211 Processing helix chain 'LV' and resid 215 through 220 removed outlier: 4.012A pdb=" N LEULV 219 " --> pdb=" O ASPLV 215 " (cutoff:3.500A) Processing helix chain 'LV' and resid 244 through 251 removed outlier: 4.292A pdb=" N ARGLV 248 " --> pdb=" O PROLV 244 " (cutoff:3.500A) Processing helix chain 'LV' and resid 266 through 274 Processing helix chain 'LV' and resid 276 through 292 removed outlier: 3.673A pdb=" N LEULV 284 " --> pdb=" O ARGLV 280 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLNLV 289 " --> pdb=" O ASPLV 285 " (cutoff:3.500A) Processing helix chain 'LV' and resid 299 through 320 Processing helix chain 'LV' and resid 415 through 423 Processing helix chain 'LV' and resid 423 through 439 removed outlier: 4.019A pdb=" N ALALV 427 " --> pdb=" O LEULV 423 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYSLV 428 " --> pdb=" O PROLV 424 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLULV 430 " --> pdb=" O TYRLV 426 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALALV 431 " --> pdb=" O ALALV 427 " (cutoff:3.500A) Processing helix chain 'LV' and resid 454 through 464 removed outlier: 3.914A pdb=" N GLNLV 458 " --> pdb=" O THRLV 454 " (cutoff:3.500A) Processing helix chain 'LV' and resid 464 through 469 removed outlier: 4.310A pdb=" N ARGLV 468 " --> pdb=" O GLYLV 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLYLV 469 " --> pdb=" O TYRLV 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 464 through 469' Processing helix chain 'LV' and resid 477 through 493 Processing helix chain 'LV' and resid 520 through 531 removed outlier: 4.178A pdb=" N LEULV 530 " --> pdb=" O ARGLV 526 " (cutoff:3.500A) Processing helix chain 'LV' and resid 549 through 566 removed outlier: 3.613A pdb=" N ARGLV 564 " --> pdb=" O ARGLV 560 " (cutoff:3.500A) Processing helix chain 'LV' and resid 580 through 588 Processing helix chain 'LV' and resid 613 through 629 Processing helix chain 'LV' and resid 640 through 662 Processing helix chain 'LV' and resid 679 through 688 removed outlier: 3.567A pdb=" N VALLV 686 " --> pdb=" O VALLV 682 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHELV 687 " --> pdb=" O GLNLV 683 " (cutoff:3.500A) Processing helix chain 'LV' and resid 702 through 706 Processing helix chain 'LV' and resid 742 through 754 removed outlier: 3.716A pdb=" N ALALV 753 " --> pdb=" O ARGLV 749 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLYLV 754 " --> pdb=" O SERLV 750 " (cutoff:3.500A) Processing helix chain 'LV' and resid 766 through 773 Processing helix chain 'LV' and resid 787 through 798 Processing helix chain 'LV' and resid 811 through 825 Processing helix chain 'LV' and resid 835 through 845 removed outlier: 3.791A pdb=" N LEULV 844 " --> pdb=" O ARGLV 840 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SERLV 845 " --> pdb=" O METLV 841 " (cutoff:3.500A) Processing helix chain 'LV' and resid 847 through 861 Processing helix chain 'LV' and resid 862 through 877 removed outlier: 3.583A pdb=" N VALLV 866 " --> pdb=" O CYSLV 862 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYSLV 877 " --> pdb=" O LEULV 873 " (cutoff:3.500A) Processing helix chain 'LV' and resid 887 through 899 removed outlier: 3.677A pdb=" N GLNLV 897 " --> pdb=" O ALALV 893 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHELV 898 " --> pdb=" O ALALV 894 " (cutoff:3.500A) Processing helix chain 'LV' and resid 903 through 918 Processing helix chain 'LV' and resid 921 through 928 Processing helix chain 'LV' and resid 931 through 953 removed outlier: 3.622A pdb=" N ARGLV 952 " --> pdb=" O METLV 948 " (cutoff:3.500A) Processing helix chain 'LV' and resid 958 through 962 removed outlier: 3.893A pdb=" N ASPLV 961 " --> pdb=" O HISLV 958 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THRLV 962 " --> pdb=" O GLULV 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 958 through 962' Processing helix chain 'LV' and resid 963 through 975 Processing helix chain 'LV' and resid 1005 through 1009 removed outlier: 3.657A pdb=" N ILELV1008 " --> pdb=" O SERLV1005 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASPLV1009 " --> pdb=" O VALLV1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 1005 through 1009' Processing helix chain 'LV' and resid 1035 through 1043 removed outlier: 4.294A pdb=" N LEULV1039 " --> pdb=" O GLULV1035 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VALLV1040 " --> pdb=" O PROLV1036 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALALV1043 " --> pdb=" O LEULV1039 " (cutoff:3.500A) Processing helix chain 'LV' and resid 1058 through 1062 removed outlier: 3.701A pdb=" N GLULV1062 " --> pdb=" O GLNLV1059 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 362 through 400 Processing helix chain 'TN' and resid 24 through 33 Processing helix chain 'TN' and resid 35 through 39 Processing sheet with id=AA1, first strand: chain 'LV' and resid 238 through 239 Processing sheet with id=AA2, first strand: chain 'LV' and resid 507 through 509 removed outlier: 6.207A pdb=" N ILELV 471 " --> pdb=" O LYSLV 517 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N METLV 519 " --> pdb=" O ILELV 471 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYSLV 473 " --> pdb=" O METLV 519 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N METLV 470 " --> pdb=" O VALLV 539 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILELV 541 " --> pdb=" O METLV 470 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALALV 472 " --> pdb=" O ILELV 541 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SERLV 538 " --> pdb=" O LYSLV 570 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N METLV 572 " --> pdb=" O SERLV 538 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILELV 540 " --> pdb=" O METLV 572 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THRLV 574 " --> pdb=" O ILELV 540 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEULV 542 " --> pdb=" O THRLV 574 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N PHELV 593 " --> pdb=" O VALLV 441 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VALLV 443 " --> pdb=" O PHELV 593 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILELV 595 " --> pdb=" O VALLV 443 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VALLV 445 " --> pdb=" O ILELV 595 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LV' and resid 669 through 673 removed outlier: 6.535A pdb=" N VALLV 634 " --> pdb=" O VALLV 698 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALALV 700 " --> pdb=" O VALLV 634 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VALLV 636 " --> pdb=" O ALALV 700 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEULV 635 " --> pdb=" O VALLV 717 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLULV 603 " --> pdb=" O CYSLV 761 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARGLV 763 " --> pdb=" O GLULV 603 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYRLV 605 " --> pdb=" O ARGLV 763 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LV' and resid 721 through 727 Processing sheet with id=AA5, first strand: chain 'LV' and resid 1019 through 1022 removed outlier: 3.728A pdb=" N ASPLV1019 " --> pdb=" O THRLV1029 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLULV1026 " --> pdb=" O GLULV 998 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SERLV 989 " --> pdb=" O VALLV 983 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1539 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: 1.50 Time building geometry restraints manager: 1.03 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: 2898 1.34 - 1.45: 1189 1.45 - 1.57: 5171 1.57 - 1.69: 11 1.69 - 1.81: 93 Bond restraints: 9362 Sorted by residual: bond pdb=" N METTN 1 " pdb=" CA METTN 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N1 URN 62 " pdb=" C2 URN 62 " ideal model delta sigma weight residual 1.381 1.392 -0.011 9.00e-03 1.23e+04 1.45e+00 bond pdb=" CB TRPLV 654 " pdb=" CG TRPLV 654 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.33e+00 bond pdb=" C PROLV 630 " pdb=" N PROLV 631 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.12e-02 7.97e+03 1.23e+00 bond pdb=" CD GLULF 485 " pdb=" OE1 GLULF 485 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.04e+00 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 12212 1.33 - 2.66: 387 2.66 - 3.98: 62 3.98 - 5.31: 44 5.31 - 6.64: 2 Bond angle restraints: 12707 Sorted by residual: angle pdb=" N1 URN 62 " pdb=" C2 URN 62 " pdb=" O2 URN 62 " ideal model delta sigma weight residual 122.80 125.96 -3.16 7.00e-01 2.04e+00 2.03e+01 angle pdb=" C1' URN 62 " pdb=" N1 URN 62 " pdb=" C2 URN 62 " ideal model delta sigma weight residual 117.70 122.65 -4.95 1.20e+00 6.94e-01 1.70e+01 angle pdb=" O5' URN 63 " pdb=" C5' URN 63 " pdb=" C4' URN 63 " ideal model delta sigma weight residual 109.40 112.69 -3.29 8.00e-01 1.56e+00 1.69e+01 angle pdb=" O2 URN 62 " pdb=" C2 URN 62 " pdb=" N3 URN 62 " ideal model delta sigma weight residual 122.20 119.39 2.81 7.00e-01 2.04e+00 1.62e+01 angle pdb=" O5' URN 65 " pdb=" C5' URN 65 " pdb=" C4' URN 65 " ideal model delta sigma weight residual 109.40 111.99 -2.59 8.00e-01 1.56e+00 1.04e+01 ... (remaining 12702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 5676 32.95 - 65.90: 88 65.90 - 98.85: 2 98.85 - 131.81: 1 131.81 - 164.76: 1 Dihedral angle restraints: 5768 sinusoidal: 2318 harmonic: 3450 Sorted by residual: dihedral pdb=" O4' URN 62 " pdb=" C1' URN 62 " pdb=" N1 URN 62 " pdb=" C2 URN 62 " ideal model delta sinusoidal sigma weight residual -160.00 4.76 -164.76 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" CA TYRLV 824 " pdb=" C TYRLV 824 " pdb=" N LEULV 825 " pdb=" CA LEULV 825 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEULV 496 " pdb=" C LEULV 496 " pdb=" N GLYLV 497 " pdb=" CA GLYLV 497 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1050 0.034 - 0.068: 302 0.068 - 0.102: 84 0.102 - 0.136: 32 0.136 - 0.169: 4 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA ARGLV 316 " pdb=" N ARGLV 316 " pdb=" C ARGLV 316 " pdb=" CB ARGLV 316 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" P URN 63 " pdb=" OP1 URN 63 " pdb=" OP2 URN 63 " pdb=" O5' URN 63 " both_signs ideal model delta sigma weight residual True 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILELV 595 " pdb=" N ILELV 595 " pdb=" C ILELV 595 " pdb=" CB ILELV 595 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1469 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPLV 654 " -0.021 2.00e-02 2.50e+03 1.46e-02 5.36e+00 pdb=" CG TRPLV 654 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRPLV 654 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRPLV 654 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPLV 654 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRPLV 654 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRPLV 654 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRPLV 654 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRPLV 654 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRPLV 654 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEULF 481 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEULF 481 " 0.030 2.00e-02 2.50e+03 pdb=" O LEULF 481 " -0.011 2.00e-02 2.50e+03 pdb=" N LEULF 482 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEULV 433 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C LEULV 433 " 0.025 2.00e-02 2.50e+03 pdb=" O LEULV 433 " -0.009 2.00e-02 2.50e+03 pdb=" N ASNLV 434 " -0.009 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1506 2.76 - 3.29: 9056 3.29 - 3.83: 14794 3.83 - 4.36: 17491 4.36 - 4.90: 29458 Nonbonded interactions: 72305 Sorted by model distance: nonbonded pdb=" O ARGLF 36 " pdb=" NE2 GLNLF 40 " model vdw 2.223 3.120 nonbonded pdb=" O LEULV 844 " pdb=" OG SERLV 845 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THRLV 639 " pdb=" OE1 GLULV 643 " model vdw 2.245 3.040 nonbonded pdb=" O PHELV 637 " pdb=" OG SERLV 719 " model vdw 2.316 3.040 nonbonded pdb=" O GLULF 97 " pdb=" OG SERLF 101 " model vdw 2.328 3.040 ... (remaining 72300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9362 Z= 0.160 Angle : 0.622 6.638 12707 Z= 0.352 Chirality : 0.038 0.169 1472 Planarity : 0.004 0.044 1638 Dihedral : 12.268 164.758 3518 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.25), residues: 1156 helix: 1.83 (0.20), residues: 641 sheet: 0.32 (0.49), residues: 117 loop : 0.35 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLV 885 TYR 0.017 0.001 TYRLV 614 PHE 0.017 0.002 PHELV 203 TRP 0.039 0.003 TRPLV 654 HIS 0.005 0.001 HISLV 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 9362) covalent geometry : angle 0.62240 / 0.35 (12707) hydrogen bonds : bond 0.14934 / 10.20 ( 522) hydrogen bonds : angle 5.68847 / 4.31 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.352 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: symmetry clash REVERT: LF 144 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7643 (mt-10) REVERT: LF 261 MET cc_start: 0.3666 (ttm) cc_final: 0.3342 (ttm) REVERT: LV 470 MET cc_start: 0.7553 (mtm) cc_final: 0.7336 (mtm) REVERT: LV 553 ASP cc_start: 0.8044 (m-30) cc_final: 0.7832 (t0) REVERT: LV 577 THR cc_start: 0.8262 (p) cc_final: 0.7933 (t) REVERT: LV 657 MET cc_start: 0.6649 (mtm) cc_final: 0.6382 (mmt) REVERT: LV 697 VAL cc_start: 0.8755 (t) cc_final: 0.8477 (m) REVERT: LV 749 ARG cc_start: 0.8872 (mtt180) cc_final: 0.8634 (mtt90) REVERT: LV 873 LEU cc_start: 0.8856 (mt) cc_final: 0.8639 (mp) REVERT: LV 915 TRP cc_start: 0.8213 (t60) cc_final: 0.7763 (t60) REVERT: TN 22 LEU cc_start: 0.7422 (mt) cc_final: 0.7083 (mt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1255 time to fit residues: 55.1870 Evaluate side-chains 190 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 439 HIS LV 620 GLN LV 731 HIS LV 789 HIS ** TN 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.168082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139358 restraints weight = 15207.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141272 restraints weight = 9149.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142285 restraints weight = 7669.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.143556 restraints weight = 5761.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143899 restraints weight = 5151.130| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9362 Z= 0.182 Angle : 0.649 11.464 12707 Z= 0.333 Chirality : 0.041 0.291 1472 Planarity : 0.005 0.049 1638 Dihedral : 8.605 149.737 1380 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.86 % Allowed : 12.61 % Favored : 84.53 % Cbeta Deviations : 0.00 % 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: 1.60 (0.24), residues: 1156 helix: 1.81 (0.19), residues: 657 sheet: 0.17 (0.52), residues: 106 loop : 0.17 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGLF 475 TYR 0.016 0.002 TYRLV 586 PHE 0.022 0.002 PHELV 203 TRP 0.014 0.002 TRPLF 155 HIS 0.005 0.001 HISLF 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9362) covalent geometry : angle 0.64932 / 0.33 (12707) hydrogen bonds : bond 0.05010 / 3.39 ( 522) hydrogen bonds : angle 4.59122 / 3.44 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 261 MET cc_start: 0.3656 (ttm) cc_final: 0.3431 (ttm) REVERT: LF 442 MET cc_start: 0.8742 (tmm) cc_final: 0.8483 (tmm) REVERT: LV 165 ARG cc_start: 0.8473 (mtm110) cc_final: 0.8182 (ptt90) REVERT: LV 250 MET cc_start: 0.8099 (ptm) cc_final: 0.7867 (ptm) REVERT: LV 609 ASP cc_start: 0.6742 (m-30) cc_final: 0.6524 (p0) REVERT: LV 657 MET cc_start: 0.6514 (mtm) cc_final: 0.6200 (mmt) REVERT: LV 697 VAL cc_start: 0.8846 (t) cc_final: 0.8540 (m) REVERT: LV 714 TYR cc_start: 0.7443 (m-80) cc_final: 0.7228 (m-80) REVERT: LV 749 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8517 (mtt180) REVERT: LV 840 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6598 (mtm-85) REVERT: LV 876 GLN cc_start: 0.8417 (tp40) cc_final: 0.7844 (tp40) REVERT: LV 915 TRP cc_start: 0.8285 (t60) cc_final: 0.7936 (t60) REVERT: TN 22 LEU cc_start: 0.7533 (mt) cc_final: 0.7146 (mt) outliers start: 27 outliers final: 16 residues processed: 214 average time/residue: 0.1033 time to fit residues: 29.9985 Evaluate side-chains 179 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 382 LEU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 622 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 840 ARG Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 18 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [54, 72, 91, 63, 19, 52, 78, 106, 65, 108, 115] chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 269 GLN LV 620 GLN LV 731 HIS ** TN 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135580 restraints weight = 15302.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137446 restraints weight = 9642.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.138316 restraints weight = 7962.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140199 restraints weight = 6103.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140468 restraints weight = 5277.677| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9362 Z= 0.161 Angle : 0.613 8.907 12707 Z= 0.314 Chirality : 0.039 0.191 1472 Planarity : 0.004 0.048 1638 Dihedral : 8.351 131.998 1380 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.07 % Allowed : 13.45 % Favored : 83.47 % Cbeta Deviations : 0.00 % 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: 1.56 (0.24), residues: 1156 helix: 1.86 (0.19), residues: 651 sheet: -0.01 (0.51), residues: 106 loop : 0.05 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLV 752 TYR 0.018 0.002 TYRLV 459 PHE 0.024 0.002 PHELF 112 TRP 0.010 0.002 TRPLV 654 HIS 0.005 0.001 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9362) covalent geometry : angle 0.61303 / 0.31 (12707) hydrogen bonds : bond 0.04528 / 3.06 ( 522) hydrogen bonds : angle 4.41943 / 3.30 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 261 MET cc_start: 0.3639 (ttm) cc_final: 0.3396 (ttm) REVERT: LF 447 LEU cc_start: 0.9027 (tt) cc_final: 0.8798 (tt) REVERT: LF 450 MET cc_start: 0.6818 (ttm) cc_final: 0.6499 (ttm) REVERT: LV 609 ASP cc_start: 0.7019 (m-30) cc_final: 0.6566 (p0) REVERT: LV 652 PHE cc_start: 0.8242 (t80) cc_final: 0.8013 (t80) REVERT: LV 657 MET cc_start: 0.6460 (mtm) cc_final: 0.6182 (mmt) REVERT: LV 697 VAL cc_start: 0.8759 (t) cc_final: 0.8503 (m) REVERT: LV 714 TYR cc_start: 0.7565 (m-80) cc_final: 0.7251 (m-80) REVERT: LV 749 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8402 (mtt180) REVERT: LV 840 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7683 (mtm-85) REVERT: LV 876 GLN cc_start: 0.8447 (tp40) cc_final: 0.7830 (tp40) REVERT: TN 22 LEU cc_start: 0.7491 (mt) cc_final: 0.7127 (mt) outliers start: 29 outliers final: 24 residues processed: 190 average time/residue: 0.1032 time to fit residues: 26.5597 Evaluate side-chains 180 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 134 GLU Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 248 SER Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 213 LEU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 433 LEU Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 622 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 840 ARG Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [88, 43, 15, 110, 86, 64, 71, 69, 78, 92, 53] chunk 88 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 455 GLN LV 620 GLN ** LV 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 932 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135053 restraints weight = 15528.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136556 restraints weight = 9205.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137332 restraints weight = 8058.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139359 restraints weight = 6156.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139483 restraints weight = 5225.865| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9362 Z= 0.141 Angle : 0.576 8.956 12707 Z= 0.298 Chirality : 0.038 0.184 1472 Planarity : 0.004 0.051 1638 Dihedral : 8.132 115.136 1380 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.97 % Allowed : 14.83 % Favored : 82.20 % Cbeta Deviations : 0.00 % 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: 1.56 (0.24), residues: 1156 helix: 1.87 (0.19), residues: 659 sheet: -0.08 (0.48), residues: 115 loop : 0.02 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLF 93 TYR 0.018 0.002 TYRLV 262 PHE 0.016 0.001 PHELV 727 TRP 0.009 0.001 TRPLV 654 HIS 0.004 0.001 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9362) covalent geometry : angle 0.57648 / 0.30 (12707) hydrogen bonds : bond 0.04159 / 2.82 ( 522) hydrogen bonds : angle 4.24670 / 3.16 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.348 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: LF 149 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7757 (ttt90) REVERT: LF 261 MET cc_start: 0.3575 (ttm) cc_final: 0.3320 (ttm) REVERT: LF 447 LEU cc_start: 0.9091 (tt) cc_final: 0.8851 (tt) REVERT: LF 485 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5267 (tm-30) REVERT: LV 223 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7766 (mtm180) REVERT: LV 553 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: LV 609 ASP cc_start: 0.7181 (m-30) cc_final: 0.6569 (p0) REVERT: LV 652 PHE cc_start: 0.8233 (t80) cc_final: 0.7989 (t80) REVERT: LV 657 MET cc_start: 0.6428 (mtm) cc_final: 0.6059 (mmt) REVERT: LV 697 VAL cc_start: 0.8776 (t) cc_final: 0.8511 (m) REVERT: LV 749 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8381 (mtt180) REVERT: LV 840 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6645 (mtm-85) REVERT: LV 876 GLN cc_start: 0.8442 (tp40) cc_final: 0.7818 (tp40) REVERT: TN 22 LEU cc_start: 0.7437 (mt) cc_final: 0.7091 (mt) outliers start: 28 outliers final: 22 residues processed: 188 average time/residue: 0.1058 time to fit residues: 27.0192 Evaluate side-chains 176 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 248 SER Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 485 GLU Chi-restraints excluded: chain LV residue 175 MET Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 553 ASP Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 622 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 840 ARG Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 18 THR Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [61, 13, 82, 113, 39, 15, 99, 110, 19, 20, 75] chunk 61 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** LV 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 620 GLN LV 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135404 restraints weight = 15730.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136956 restraints weight = 9298.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138227 restraints weight = 7903.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138866 restraints weight = 6119.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139525 restraints weight = 5793.786| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9362 Z= 0.152 Angle : 0.579 9.339 12707 Z= 0.297 Chirality : 0.039 0.219 1472 Planarity : 0.004 0.054 1638 Dihedral : 8.028 106.260 1380 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.28 % Allowed : 16.74 % Favored : 79.98 % Cbeta Deviations : 0.00 % 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: 1.55 (0.24), residues: 1156 helix: 1.88 (0.19), residues: 659 sheet: -0.16 (0.49), residues: 113 loop : -0.00 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGLV 896 TYR 0.014 0.002 TYRLV 715 PHE 0.018 0.002 PHELV 727 TRP 0.008 0.001 TRPLV 654 HIS 0.007 0.001 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9362) covalent geometry : angle 0.57933 / 0.30 (12707) hydrogen bonds : bond 0.04067 / 2.77 ( 522) hydrogen bonds : angle 4.19109 / 3.12 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 149 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7826 (ttt90) REVERT: LF 261 MET cc_start: 0.3779 (ttm) cc_final: 0.3144 (ttp) REVERT: LF 447 LEU cc_start: 0.9160 (tt) cc_final: 0.8924 (tt) REVERT: LF 485 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5272 (tm-30) REVERT: LV 223 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7802 (mtm180) REVERT: LV 245 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7587 (ptm-80) REVERT: LV 470 MET cc_start: 0.7591 (mtt) cc_final: 0.7319 (mtm) REVERT: LV 609 ASP cc_start: 0.7652 (m-30) cc_final: 0.6855 (p0) REVERT: LV 652 PHE cc_start: 0.8210 (t80) cc_final: 0.7970 (t80) REVERT: LV 657 MET cc_start: 0.6598 (mtm) cc_final: 0.6210 (mmt) REVERT: LV 670 MET cc_start: 0.7394 (tpt) cc_final: 0.7156 (tpp) REVERT: LV 749 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8355 (mtt180) REVERT: LV 876 GLN cc_start: 0.8365 (tp40) cc_final: 0.7734 (tp40) REVERT: TN 22 LEU cc_start: 0.7464 (mt) cc_final: 0.7104 (mt) outliers start: 31 outliers final: 24 residues processed: 183 average time/residue: 0.1056 time to fit residues: 26.2306 Evaluate side-chains 174 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 248 SER Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 485 GLU Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 433 LEU Chi-restraints excluded: chain LV residue 456 ILE Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 529 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 622 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [50, 10, 87, 72, 103, 31, 26, 0, 16, 81, 36] chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LF 130 HIS LV 620 GLN TN 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134515 restraints weight = 15548.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135988 restraints weight = 9207.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137220 restraints weight = 7891.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137991 restraints weight = 6064.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138614 restraints weight = 5704.133| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9362 Z= 0.176 Angle : 0.612 15.560 12707 Z= 0.309 Chirality : 0.039 0.214 1472 Planarity : 0.004 0.056 1638 Dihedral : 8.023 105.727 1380 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.92 % Allowed : 16.53 % Favored : 79.56 % Cbeta Deviations : 0.00 % 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: 1.44 (0.24), residues: 1156 helix: 1.79 (0.19), residues: 658 sheet: -0.13 (0.50), residues: 113 loop : -0.06 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLF 93 TYR 0.015 0.002 TYRLV 715 PHE 0.018 0.002 PHELV 203 TRP 0.008 0.001 TRPLV 654 HIS 0.004 0.001 HISLV 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 9362) covalent geometry : angle 0.61188 / 0.31 (12707) hydrogen bonds : bond 0.04175 / 2.86 ( 522) hydrogen bonds : angle 4.22459 / 3.13 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.622 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: LF 149 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7776 (ttt90) REVERT: LF 261 MET cc_start: 0.3883 (ttm) cc_final: 0.3212 (ttp) REVERT: LF 485 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5349 (tm-30) REVERT: LV 269 GLN cc_start: 0.7649 (mt0) cc_final: 0.6926 (mp10) REVERT: LV 470 MET cc_start: 0.7667 (mtt) cc_final: 0.7425 (mtm) REVERT: LV 506 PHE cc_start: 0.7535 (m-80) cc_final: 0.7139 (m-80) REVERT: LV 657 MET cc_start: 0.6546 (mtm) cc_final: 0.6150 (mmt) REVERT: LV 749 ARG cc_start: 0.8832 (mtt180) cc_final: 0.8362 (mtt180) REVERT: LV 797 MET cc_start: 0.7790 (mmm) cc_final: 0.7565 (mmp) REVERT: LV 876 GLN cc_start: 0.8313 (tp40) cc_final: 0.7700 (tp40) REVERT: TN 22 LEU cc_start: 0.7507 (mt) cc_final: 0.7195 (mt) outliers start: 37 outliers final: 30 residues processed: 177 average time/residue: 0.0968 time to fit residues: 23.7650 Evaluate side-chains 178 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 85 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 248 SER Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 485 GLU Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 433 LEU Chi-restraints excluded: chain LV residue 456 ILE Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 525 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 584 CYS Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 622 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 710 ILE Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 925 CYS Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 18 THR Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [46, 49, 110, 36, 23, 34, 15, 64, 106, 8, 16] chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 8 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136285 restraints weight = 15628.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137647 restraints weight = 9284.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139036 restraints weight = 7918.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139632 restraints weight = 6057.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140378 restraints weight = 5787.513| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9362 Z= 0.127 Angle : 0.590 12.339 12707 Z= 0.294 Chirality : 0.038 0.214 1472 Planarity : 0.004 0.057 1638 Dihedral : 7.924 106.303 1380 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.18 % Allowed : 16.95 % Favored : 79.87 % Cbeta Deviations : 0.00 % 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: 1.59 (0.24), residues: 1156 helix: 1.95 (0.19), residues: 655 sheet: -0.10 (0.50), residues: 113 loop : -0.06 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGLV 896 TYR 0.012 0.001 TYRLV 715 PHE 0.030 0.001 PHELV 652 TRP 0.008 0.001 TRPLV 654 HIS 0.002 0.001 HISLF 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9362) covalent geometry : angle 0.59005 / 0.29 (12707) hydrogen bonds : bond 0.03825 / 2.62 ( 522) hydrogen bonds : angle 4.06200 / 3.00 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 94 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8024 (mm) REVERT: LF 149 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7820 (ttt90) REVERT: LF 152 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8500 (tt) REVERT: LF 261 MET cc_start: 0.3749 (ttm) cc_final: 0.3116 (ttp) REVERT: LF 442 MET cc_start: 0.8928 (tmm) cc_final: 0.8562 (tmm) REVERT: LF 485 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5349 (tm-30) REVERT: LV 470 MET cc_start: 0.7649 (mtt) cc_final: 0.7369 (mtm) REVERT: LV 506 PHE cc_start: 0.7531 (m-80) cc_final: 0.7117 (m-80) REVERT: LV 642 GLU cc_start: 0.8245 (pm20) cc_final: 0.8014 (pm20) REVERT: LV 657 MET cc_start: 0.6408 (mtm) cc_final: 0.6078 (mmt) REVERT: LV 670 MET cc_start: 0.7334 (tpt) cc_final: 0.7089 (tpp) REVERT: LV 749 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8398 (mtt180) REVERT: LV 797 MET cc_start: 0.7777 (mmm) cc_final: 0.7536 (mmp) REVERT: LV 876 GLN cc_start: 0.8291 (tp40) cc_final: 0.7637 (tp40) REVERT: TN 22 LEU cc_start: 0.7556 (mt) cc_final: 0.7218 (mt) outliers start: 30 outliers final: 25 residues processed: 178 average time/residue: 0.0946 time to fit residues: 23.3857 Evaluate side-chains 176 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 85 VAL Chi-restraints excluded: chain LF residue 94 LEU Chi-restraints excluded: chain LF residue 152 LEU Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 248 SER Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 485 GLU Chi-restraints excluded: chain LV residue 195 MET Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 529 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 584 CYS Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 835 THR Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [32, 16, 29, 91, 17, 108, 84, 67, 27, 39, 114] chunk 32 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134877 restraints weight = 15516.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136443 restraints weight = 9255.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137693 restraints weight = 7908.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138361 restraints weight = 6018.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138995 restraints weight = 5694.462| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9362 Z= 0.156 Angle : 0.599 11.963 12707 Z= 0.301 Chirality : 0.039 0.206 1472 Planarity : 0.004 0.058 1638 Dihedral : 7.909 106.124 1380 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.50 % Allowed : 17.48 % Favored : 79.03 % Cbeta Deviations : 0.00 % 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: 1.56 (0.24), residues: 1156 helix: 1.91 (0.19), residues: 656 sheet: -0.16 (0.51), residues: 113 loop : -0.02 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLF 93 TYR 0.011 0.001 TYRLV 614 PHE 0.030 0.002 PHELV 652 TRP 0.008 0.001 TRPLV 654 HIS 0.005 0.001 HISLV 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9362) covalent geometry : angle 0.59855 / 0.30 (12707) hydrogen bonds : bond 0.03968 / 2.72 ( 522) hydrogen bonds : angle 4.11415 / 3.04 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 94 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8036 (mm) REVERT: LF 149 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7837 (ttt90) REVERT: LF 261 MET cc_start: 0.3770 (ttm) cc_final: 0.3161 (ttp) REVERT: LF 485 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5337 (tm-30) REVERT: LV 223 ARG cc_start: 0.8076 (mpp80) cc_final: 0.7805 (mpp80) REVERT: LV 470 MET cc_start: 0.7695 (mtt) cc_final: 0.7450 (mtm) REVERT: LV 506 PHE cc_start: 0.7633 (m-80) cc_final: 0.7195 (m-80) REVERT: LV 657 MET cc_start: 0.6414 (mtm) cc_final: 0.6086 (mmt) REVERT: LV 670 MET cc_start: 0.7373 (tpt) cc_final: 0.7128 (tpp) REVERT: LV 797 MET cc_start: 0.7829 (mmm) cc_final: 0.7553 (mmp) REVERT: LV 876 GLN cc_start: 0.8289 (tp40) cc_final: 0.7499 (tp40) REVERT: TN 22 LEU cc_start: 0.7387 (mt) cc_final: 0.7079 (mt) outliers start: 33 outliers final: 28 residues processed: 172 average time/residue: 0.0954 time to fit residues: 22.7126 Evaluate side-chains 176 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 85 VAL Chi-restraints excluded: chain LF residue 94 LEU Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 485 GLU Chi-restraints excluded: chain LV residue 195 MET Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 433 LEU Chi-restraints excluded: chain LV residue 456 ILE Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 584 CYS Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 710 ILE Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 925 CYS Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [97, 56, 5, 4, 24, 84, 30, 35, 62, 106, 19] chunk 97 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133592 restraints weight = 15557.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134938 restraints weight = 9309.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136143 restraints weight = 8076.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137042 restraints weight = 6177.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137634 restraints weight = 5728.319| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9362 Z= 0.166 Angle : 0.616 11.122 12707 Z= 0.313 Chirality : 0.039 0.206 1472 Planarity : 0.004 0.058 1638 Dihedral : 7.906 105.932 1380 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.39 % Allowed : 17.80 % Favored : 78.81 % Cbeta Deviations : 0.00 % 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: 1.53 (0.24), residues: 1156 helix: 1.88 (0.19), residues: 656 sheet: -0.24 (0.49), residues: 113 loop : -0.00 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLF 93 TYR 0.012 0.002 TYRLV 614 PHE 0.027 0.002 PHELV 652 TRP 0.008 0.001 TRPLV 654 HIS 0.003 0.001 HISLV 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9362) covalent geometry : angle 0.61589 / 0.31 (12707) hydrogen bonds : bond 0.04040 / 2.76 ( 522) hydrogen bonds : angle 4.16613 / 3.07 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 94 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7927 (mm) REVERT: LF 149 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7879 (ttt90) REVERT: LF 261 MET cc_start: 0.3961 (ttm) cc_final: 0.3394 (ttp) REVERT: LV 223 ARG cc_start: 0.8088 (mpp80) cc_final: 0.7784 (mpp80) REVERT: LV 506 PHE cc_start: 0.7597 (m-80) cc_final: 0.7163 (m-80) REVERT: LV 656 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6332 (tt0) REVERT: LV 657 MET cc_start: 0.6386 (mtm) cc_final: 0.6105 (mmt) REVERT: LV 670 MET cc_start: 0.7428 (tpt) cc_final: 0.7180 (tpp) REVERT: LV 797 MET cc_start: 0.7796 (mmm) cc_final: 0.7508 (mmp) REVERT: LV 876 GLN cc_start: 0.8309 (tp40) cc_final: 0.7504 (tp40) REVERT: LV 984 ASP cc_start: 0.6081 (t0) cc_final: 0.5874 (t70) REVERT: TN 22 LEU cc_start: 0.7504 (mt) cc_final: 0.7159 (mt) outliers start: 32 outliers final: 28 residues processed: 173 average time/residue: 0.0976 time to fit residues: 23.5573 Evaluate side-chains 179 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 85 VAL Chi-restraints excluded: chain LF residue 94 LEU Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 456 ILE Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 529 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 584 CYS Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 710 ILE Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 835 THR Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 925 CYS Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [51, 32, 54, 29, 114, 76, 55, 58, 57, 0, 67] chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 54 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LF 488 GLN LV 417 GLN LV 620 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135982 restraints weight = 15532.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137462 restraints weight = 9120.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138649 restraints weight = 7827.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139436 restraints weight = 5949.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140035 restraints weight = 5561.523| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9362 Z= 0.132 Angle : 0.619 11.976 12707 Z= 0.309 Chirality : 0.039 0.216 1472 Planarity : 0.004 0.058 1638 Dihedral : 7.825 106.249 1380 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.07 % Allowed : 18.96 % Favored : 77.97 % Cbeta Deviations : 0.00 % 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: 1.58 (0.25), residues: 1156 helix: 1.94 (0.19), residues: 659 sheet: -0.17 (0.50), residues: 111 loop : -0.06 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLF 93 TYR 0.010 0.001 TYRLV 614 PHE 0.033 0.001 PHELV 652 TRP 0.007 0.001 TRPLV 654 HIS 0.003 0.001 HISLV 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9362) covalent geometry : angle 0.61863 / 0.31 (12707) hydrogen bonds : bond 0.03830 / 2.60 ( 522) hydrogen bonds : angle 4.08323 / 3.02 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 94 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7997 (mm) REVERT: LF 149 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7838 (ttt90) REVERT: LF 261 MET cc_start: 0.3747 (ttm) cc_final: 0.3355 (ttp) REVERT: LF 442 MET cc_start: 0.8849 (tmm) cc_final: 0.8639 (tmm) REVERT: LV 162 GLU cc_start: 0.6183 (mp0) cc_final: 0.5958 (mp0) REVERT: LV 223 ARG cc_start: 0.8068 (mpp80) cc_final: 0.7789 (mpp80) REVERT: LV 269 GLN cc_start: 0.7471 (mt0) cc_final: 0.6683 (mp10) REVERT: LV 506 PHE cc_start: 0.7517 (m-80) cc_final: 0.7105 (m-80) REVERT: LV 657 MET cc_start: 0.6354 (mtm) cc_final: 0.6115 (mmt) REVERT: LV 670 MET cc_start: 0.7401 (tpt) cc_final: 0.7155 (tpp) REVERT: LV 797 MET cc_start: 0.7757 (mmm) cc_final: 0.7505 (mmp) REVERT: LV 876 GLN cc_start: 0.8301 (tp40) cc_final: 0.7454 (tp40) REVERT: TN 22 LEU cc_start: 0.7418 (mt) cc_final: 0.7088 (mt) outliers start: 29 outliers final: 26 residues processed: 177 average time/residue: 0.1033 time to fit residues: 24.8336 Evaluate side-chains 176 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 46 TRP Chi-restraints excluded: chain LF residue 65 VAL Chi-restraints excluded: chain LF residue 85 VAL Chi-restraints excluded: chain LF residue 94 LEU Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 232 LEU Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LV residue 181 THR Chi-restraints excluded: chain LV residue 197 VAL Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 513 LEU Chi-restraints excluded: chain LV residue 525 LEU Chi-restraints excluded: chain LV residue 529 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 584 CYS Chi-restraints excluded: chain LV residue 604 THR Chi-restraints excluded: chain LV residue 615 VAL Chi-restraints excluded: chain LV residue 634 VAL Chi-restraints excluded: chain LV residue 644 ILE Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 844 LEU Chi-restraints excluded: chain LV residue 1022 MET Chi-restraints excluded: chain LV residue 1023 THR Chi-restraints excluded: chain LV residue 1051 LYS Chi-restraints excluded: chain TN residue 2 ASP Chi-restraints excluded: chain TN residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: [103, 72, 5, 96, 20, 40, 78, 70, 59, 22, 89] chunk 103 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.161180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133136 restraints weight = 15472.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135103 restraints weight = 9622.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135971 restraints weight = 7789.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137912 restraints weight = 6006.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138074 restraints weight = 5221.096| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9362 Z= 0.146 Angle : 0.618 11.992 12707 Z= 0.311 Chirality : 0.039 0.206 1472 Planarity : 0.004 0.056 1638 Dihedral : 7.790 106.239 1380 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.39 % Allowed : 18.86 % Favored : 77.75 % Cbeta Deviations : 0.00 % 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: 1.54 (0.24), residues: 1156 helix: 1.89 (0.19), residues: 659 sheet: -0.15 (0.50), residues: 111 loop : -0.06 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLF 93 TYR 0.011 0.001 TYRLV 614 PHE 0.030 0.001 PHELV 652 TRP 0.007 0.001 TRPLV 654 HIS 0.003 0.001 HISLV 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9362) covalent geometry : angle 0.61799 / 0.31 (12707) hydrogen bonds : bond 0.03852 / 2.62 ( 522) hydrogen bonds : angle 4.10450 / 3.04 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.71 seconds wall clock time: 29 minutes 2.79 seconds (1742.79 seconds total)