Starting phenix.real_space_refine on Wed Feb 14 18:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijm_35489/02_2024/8ijm_35489_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 49 5.16 5 Na 2 4.78 5 C 6435 2.51 5 N 1638 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7592 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2215 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 252} Chain breaks: 1 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {' NA': 2, 'ACP': 1, 'CLR': 1, 'PCW': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.08, per 1000 atoms: 0.61 Number of scatterers: 9982 At special positions: 0 Unit cell: (72.21, 98.355, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 5 15.00 Na 2 11.00 O 1853 8.00 N 1638 7.00 C 6435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 10 sheets defined 39.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.620A pdb=" N GLN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.048A pdb=" N GLU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.892A pdb=" N ILE A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 161 Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 295 through 324 removed outlier: 4.234A pdb=" N CYS A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 349 through 365 Processing helix chain 'A' and resid 373 through 381 removed outlier: 4.502A pdb=" N GLY A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.723A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.758A pdb=" N SER A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.527A pdb=" N SER A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 669 through 671 No H-bonds generated for 'chain 'A' and resid 669 through 671' Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.809A pdb=" N GLN A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 769 through 795 removed outlier: 3.592A pdb=" N VAL A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 791 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.560A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 835 removed outlier: 4.015A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 886 removed outlier: 3.603A pdb=" N GLY A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 944 through 947 No H-bonds generated for 'chain 'A' and resid 944 through 947' Processing helix chain 'A' and resid 956 through 959 No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 966 through 983 Processing helix chain 'A' and resid 998 through 1002 removed outlier: 3.777A pdb=" N TRP A1001 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1024 removed outlier: 3.555A pdb=" N ILE A1011 " --> pdb=" O HIS A1007 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A1021 " --> pdb=" O MET A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1033 No H-bonds generated for 'chain 'A' and resid 1030 through 1033' Processing helix chain 'B' and resid 38 through 60 removed outlier: 3.508A pdb=" N TYR B 43 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.540A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.830A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing sheet with id= A, first strand: chain 'A' and resid 182 through 185 removed outlier: 4.285A pdb=" N VAL A 183 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 192 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 190 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 202 through 206 removed outlier: 6.239A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 368 through 370 Processing sheet with id= D, first strand: chain 'A' and resid 624 through 627 Processing sheet with id= E, first strand: chain 'A' and resid 408 through 411 removed outlier: 7.202A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 521 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 519 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 518 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= G, first strand: chain 'A' and resid 674 through 677 removed outlier: 6.629A pdb=" N GLU A 699 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 677 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 701 " --> pdb=" O VAL A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.621A pdb=" N ASN B 227 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 91 removed outlier: 7.946A pdb=" N ILE B 88 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS B 299 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE B 90 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B 301 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 209 through 211 327 hydrogen bonds defined for protein. 882 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: 2.91 Time building geometry restraints manager: 4.69 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: 3154 1.34 - 1.46: 2142 1.46 - 1.58: 4795 1.58 - 1.70: 10 1.70 - 1.82: 80 Bond restraints: 10181 Sorted by residual: bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C11 PCW A1102 " pdb=" O3 PCW A1102 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C31 PCW A1103 " pdb=" O2 PCW A1103 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C31 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sigma weight residual 1.333 1.453 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 10176 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.88: 289 106.88 - 114.16: 5991 114.16 - 121.45: 5055 121.45 - 128.73: 2403 128.73 - 136.01: 55 Bond angle restraints: 13793 Sorted by residual: angle pdb=" N ILE A 940 " pdb=" CA ILE A 940 " pdb=" C ILE A 940 " ideal model delta sigma weight residual 112.96 107.32 5.64 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sigma weight residual 116.30 131.38 -15.08 3.50e+00 8.16e-02 1.86e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 109.76 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N GLY B 248 " pdb=" CA GLY B 248 " pdb=" C GLY B 248 " ideal model delta sigma weight residual 113.18 121.49 -8.31 2.37e+00 1.78e-01 1.23e+01 angle pdb=" CB MET A 680 " pdb=" CG MET A 680 " pdb=" SD MET A 680 " ideal model delta sigma weight residual 112.70 123.00 -10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 13788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 5923 28.29 - 56.59: 281 56.59 - 84.88: 19 84.88 - 113.18: 6 113.18 - 141.47: 1 Dihedral angle restraints: 6230 sinusoidal: 2617 harmonic: 3613 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 -178.43 -88.57 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 144.76 -51.76 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1193 0.047 - 0.094: 298 0.094 - 0.141: 78 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C2 PCW A1102 " pdb=" C1 PCW A1102 " pdb=" C3 PCW A1102 " pdb=" O2 PCW A1102 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 1572 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.047 2.00e-02 2.50e+03 3.86e-02 1.86e+01 pdb=" C7 NAG B 401 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.061 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 94 " 0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO B 95 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 95 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 96 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.047 5.00e-02 4.00e+02 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1449 2.76 - 3.29: 9669 3.29 - 3.83: 16301 3.83 - 4.36: 19740 4.36 - 4.90: 33578 Nonbonded interactions: 80737 Sorted by model distance: nonbonded pdb=" OG1 THR A 686 " pdb=" OE1 GLN A 689 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 695 " pdb=" OE1 GLN A 720 " model vdw 2.247 2.440 nonbonded pdb=" OG SER A 503 " pdb=" O VAL A 518 " model vdw 2.250 2.440 nonbonded pdb=" NH2 ARG A 619 " pdb=" O GLY A 644 " model vdw 2.256 2.520 nonbonded pdb=" O PHE A 256 " pdb=" OG1 THR A 259 " model vdw 2.267 2.440 ... (remaining 80732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 6.160 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.710 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.005 0.129 10181 Z= 0.315 Angle : 0.780 15.080 13793 Z= 0.385 Chirality : 0.044 0.235 1575 Planarity : 0.005 0.085 1733 Dihedral : 15.625 141.471 3899 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 0.93 % Allowed : 12.95 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1240 helix: -0.45 (0.23), residues: 517 sheet: -0.34 (0.44), residues: 136 loop : -0.73 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.023 0.001 PHE A 105 TYR 0.014 0.001 TYR A 881 ARG 0.004 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.223 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.2392 time to fit residues: 25.0259 Evaluate side-chains 69 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 946 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 650 ASN A 941 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10181 Z= 0.202 Angle : 0.570 12.400 13793 Z= 0.291 Chirality : 0.043 0.186 1575 Planarity : 0.005 0.085 1733 Dihedral : 9.383 125.651 1561 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 2.33 % Allowed : 11.93 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1240 helix: -0.17 (0.23), residues: 524 sheet: -0.14 (0.44), residues: 134 loop : -0.69 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.016 0.001 PHE B 296 TYR 0.017 0.001 TYR A 881 ARG 0.005 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 746 MET cc_start: 0.8028 (mmm) cc_final: 0.7802 (mmm) REVERT: B 91 ARG cc_start: 0.7398 (ttt90) cc_final: 0.7091 (ttt180) REVERT: B 96 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8351 (mttp) REVERT: B 99 GLU cc_start: 0.7614 (tp30) cc_final: 0.7201 (tt0) REVERT: B 266 ASN cc_start: 0.8321 (t0) cc_final: 0.8107 (t0) outliers start: 25 outliers final: 16 residues processed: 93 average time/residue: 0.2227 time to fit residues: 30.3336 Evaluate side-chains 85 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 31 optimal weight: 0.0670 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10181 Z= 0.190 Angle : 0.545 12.203 13793 Z= 0.278 Chirality : 0.042 0.172 1575 Planarity : 0.005 0.085 1733 Dihedral : 9.012 131.618 1554 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.08 % Allowed : 12.77 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1240 helix: -0.05 (0.24), residues: 518 sheet: -0.29 (0.43), residues: 135 loop : -0.66 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.012 0.001 PHE B 296 TYR 0.017 0.001 TYR A 881 ARG 0.005 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.121 Fit side-chains REVERT: A 176 MET cc_start: 0.1143 (mmp) cc_final: 0.0854 (mmt) REVERT: A 950 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8264 (mtpt) REVERT: A 999 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: B 96 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8369 (mttp) REVERT: B 99 GLU cc_start: 0.7508 (tp30) cc_final: 0.7136 (tt0) outliers start: 33 outliers final: 17 residues processed: 101 average time/residue: 0.2223 time to fit residues: 32.7147 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10181 Z= 0.265 Angle : 0.581 12.747 13793 Z= 0.294 Chirality : 0.044 0.167 1575 Planarity : 0.005 0.084 1733 Dihedral : 9.049 139.883 1550 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 3.73 % Allowed : 12.86 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1240 helix: -0.04 (0.24), residues: 517 sheet: -0.37 (0.41), residues: 145 loop : -0.73 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.014 0.002 PHE B 296 TYR 0.019 0.002 TYR A 881 ARG 0.004 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 80 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8311 (mtpt) REVERT: A 999 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: B 96 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: B 99 GLU cc_start: 0.7545 (tp30) cc_final: 0.7157 (tt0) outliers start: 40 outliers final: 23 residues processed: 107 average time/residue: 0.2212 time to fit residues: 34.3560 Evaluate side-chains 100 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 0.0070 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10181 Z= 0.229 Angle : 0.563 13.354 13793 Z= 0.285 Chirality : 0.043 0.176 1575 Planarity : 0.005 0.083 1733 Dihedral : 9.041 143.289 1550 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.82 % Allowed : 13.89 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1240 helix: 0.03 (0.24), residues: 518 sheet: -0.43 (0.41), residues: 145 loop : -0.73 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.010 0.001 HIS A 632 PHE 0.013 0.001 PHE B 108 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 75 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 417 ASN cc_start: 0.4580 (OUTLIER) cc_final: 0.3512 (m-40) REVERT: A 950 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8324 (mtpt) REVERT: A 999 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: B 96 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8353 (mttp) REVERT: B 99 GLU cc_start: 0.7541 (tp30) cc_final: 0.7154 (tt0) outliers start: 41 outliers final: 26 residues processed: 103 average time/residue: 0.2165 time to fit residues: 32.4787 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10181 Z= 0.249 Angle : 0.572 13.658 13793 Z= 0.288 Chirality : 0.043 0.175 1575 Planarity : 0.005 0.082 1733 Dihedral : 9.128 146.600 1550 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 3.82 % Allowed : 14.63 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1240 helix: 0.07 (0.24), residues: 518 sheet: -0.53 (0.41), residues: 143 loop : -0.75 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.020 0.002 PHE A 500 TYR 0.018 0.002 TYR A 881 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 74 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 333 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 950 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8062 (mtpt) REVERT: B 96 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (mttp) REVERT: B 99 GLU cc_start: 0.7540 (tp30) cc_final: 0.7158 (tt0) outliers start: 41 outliers final: 33 residues processed: 100 average time/residue: 0.2197 time to fit residues: 31.9145 Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 73 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10181 Z= 0.204 Angle : 0.566 14.304 13793 Z= 0.283 Chirality : 0.043 0.180 1575 Planarity : 0.004 0.082 1733 Dihedral : 9.048 147.834 1550 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 3.45 % Allowed : 15.56 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1240 helix: 0.17 (0.24), residues: 518 sheet: -0.45 (0.41), residues: 141 loop : -0.72 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.015 0.001 PHE A 500 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: A 999 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (pm20) REVERT: B 96 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8296 (mttp) REVERT: B 99 GLU cc_start: 0.7506 (tp30) cc_final: 0.7120 (tt0) outliers start: 37 outliers final: 28 residues processed: 102 average time/residue: 0.2104 time to fit residues: 31.8489 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10181 Z= 0.185 Angle : 0.557 14.627 13793 Z= 0.279 Chirality : 0.042 0.180 1575 Planarity : 0.004 0.082 1733 Dihedral : 8.902 147.662 1550 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 16.50 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1240 helix: 0.29 (0.24), residues: 516 sheet: -0.59 (0.41), residues: 150 loop : -0.64 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.011 0.001 HIS A 632 PHE 0.019 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.002 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: A 999 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: B 96 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 99 GLU cc_start: 0.7428 (tp30) cc_final: 0.7101 (tt0) outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 0.2304 time to fit residues: 32.3488 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 100 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10181 Z= 0.181 Angle : 0.551 14.847 13793 Z= 0.275 Chirality : 0.042 0.183 1575 Planarity : 0.004 0.081 1733 Dihedral : 8.806 147.888 1550 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 3.45 % Allowed : 16.03 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1240 helix: 0.39 (0.25), residues: 515 sheet: -0.61 (0.42), residues: 140 loop : -0.64 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.010 0.001 HIS A 632 PHE 0.018 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.002 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 74 time to evaluate : 1.013 Fit side-chains REVERT: A 950 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: A 999 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: B 96 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 99 GLU cc_start: 0.7416 (tp30) cc_final: 0.7092 (tt0) outliers start: 37 outliers final: 29 residues processed: 98 average time/residue: 0.2228 time to fit residues: 32.2901 Evaluate side-chains 106 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 78 optimal weight: 0.4980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10181 Z= 0.209 Angle : 0.566 14.909 13793 Z= 0.282 Chirality : 0.043 0.183 1575 Planarity : 0.004 0.081 1733 Dihedral : 8.805 150.533 1550 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.17 % Allowed : 16.31 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1240 helix: 0.42 (0.24), residues: 518 sheet: -0.56 (0.42), residues: 140 loop : -0.66 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.017 0.001 PHE A 105 TYR 0.017 0.001 TYR A 881 ARG 0.002 0.000 ARG B 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 74 time to evaluate : 1.191 Fit side-chains REVERT: A 950 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8077 (mtpt) REVERT: A 999 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: B 96 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: B 99 GLU cc_start: 0.7423 (tp30) cc_final: 0.7098 (tt0) outliers start: 34 outliers final: 29 residues processed: 95 average time/residue: 0.2220 time to fit residues: 30.9795 Evaluate side-chains 104 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 0.0370 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.233165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.210864 restraints weight = 10560.480| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 0.97 r_work: 0.4111 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10181 Z= 0.201 Angle : 0.568 15.069 13793 Z= 0.283 Chirality : 0.043 0.187 1575 Planarity : 0.004 0.081 1733 Dihedral : 8.758 152.458 1550 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.45 % Allowed : 15.94 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1240 helix: 0.48 (0.25), residues: 517 sheet: -0.48 (0.42), residues: 140 loop : -0.64 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.016 0.001 PHE A 105 TYR 0.017 0.001 TYR A 881 ARG 0.002 0.000 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.94 seconds wall clock time: 39 minutes 26.23 seconds (2366.23 seconds total)