Starting phenix.real_space_refine on Thu May 1 05:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdq_52072/05_2025/9hdq_52072.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Zn 1 6.06 5 P 85 5.49 5 S 39 5.16 5 C 6349 2.51 5 N 1770 2.21 5 O 2017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10261 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8505 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 43, 'TRANS': 981} Chain: "B" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "E" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7304 SG CYS A1130 39.917 77.107 104.187 1.00 67.00 S ATOM 7339 SG CYS A1134 41.652 76.706 107.716 1.00 67.85 S ATOM 7445 SG CYS A1147 42.901 74.525 104.815 1.00 57.58 S Time building chain proxies: 6.89, per 1000 atoms: 0.67 Number of scatterers: 10261 At special positions: 0 Unit cell: (92.635, 146.115, 119.375, 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) Zn 1 29.99 S 39 16.00 P 85 15.00 O 2017 8.00 N 1770 7.00 C 6349 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1134 " Number of angles added : 3 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 67.4% alpha, 6.9% beta 36 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.856A pdb=" N ASN A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'A' and resid 259 through 278 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.566A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.693A pdb=" N SER A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 370 removed outlier: 3.734A pdb=" N ARG A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 removed outlier: 3.599A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.514A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.099A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.614A pdb=" N SER A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.652A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 559 removed outlier: 3.517A pdb=" N GLN A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 558 " --> pdb=" O HIS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.585A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 621 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.727A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.128A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 800 removed outlier: 4.383A pdb=" N LYS A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 805 through 828 removed outlier: 4.033A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 833 through 849 removed outlier: 4.096A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 4.240A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.867A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 967 removed outlier: 3.911A pdb=" N LEU A 967 " --> pdb=" O TRP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.658A pdb=" N ASP A 993 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1006 removed outlier: 3.766A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.930A pdb=" N ILE A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.899A pdb=" N ARG A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 removed outlier: 3.850A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.641A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.598A pdb=" N MET A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.504A pdb=" N TRP A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1181 through 1185 removed outlier: 3.561A pdb=" N LYS A1185 " --> pdb=" O ASN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1206 removed outlier: 3.575A pdb=" N ARG A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.568A pdb=" N TYR A1232 " --> pdb=" O THR A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 4.740A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.834A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.834A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 removed outlier: 4.190A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 768 485 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2211 1.33 - 1.45: 2711 1.45 - 1.58: 5514 1.58 - 1.70: 164 1.70 - 1.82: 63 Bond restraints: 10663 Sorted by residual: bond pdb=" P DA F 1 " pdb=" OP1 DA F 1 " ideal model delta sigma weight residual 1.480 1.546 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" P DT E 25 " pdb=" OP1 DT E 25 " ideal model delta sigma weight residual 1.480 1.528 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" P DA F 1 " pdb=" OP2 DA F 1 " ideal model delta sigma weight residual 1.480 1.528 -0.048 2.00e-02 2.50e+03 5.64e+00 bond pdb=" P DA G 1 " pdb=" OP2 DA G 1 " ideal model delta sigma weight residual 1.480 1.524 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" P DA G 1 " pdb=" OP1 DA G 1 " ideal model delta sigma weight residual 1.480 1.524 -0.044 2.00e-02 2.50e+03 4.84e+00 ... (remaining 10658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12629 1.57 - 3.13: 1811 3.13 - 4.70: 265 4.70 - 6.27: 31 6.27 - 7.83: 10 Bond angle restraints: 14746 Sorted by residual: angle pdb=" CA TYR A 914 " pdb=" CB TYR A 914 " pdb=" CG TYR A 914 " ideal model delta sigma weight residual 113.90 106.07 7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C4' DA F 2 " pdb=" C3' DA F 2 " pdb=" O3' DA F 2 " ideal model delta sigma weight residual 110.00 103.65 6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N TRP A1158 " pdb=" CA TRP A1158 " pdb=" C TRP A1158 " ideal model delta sigma weight residual 111.71 116.44 -4.73 1.15e+00 7.56e-01 1.69e+01 angle pdb=" N ALA A 420 " pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 111.36 115.62 -4.26 1.09e+00 8.42e-01 1.52e+01 angle pdb=" C4' DA F 5 " pdb=" C3' DA F 5 " pdb=" O3' DA F 5 " ideal model delta sigma weight residual 110.00 104.37 5.63 1.50e+00 4.44e-01 1.41e+01 ... (remaining 14741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 5866 33.08 - 66.15: 445 66.15 - 99.23: 18 99.23 - 132.30: 0 132.30 - 165.37: 1 Dihedral angle restraints: 6330 sinusoidal: 3290 harmonic: 3040 Sorted by residual: dihedral pdb=" CA ASP A 993 " pdb=" C ASP A 993 " pdb=" N PHE A 994 " pdb=" CA PHE A 994 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU A 953 " pdb=" C LEU A 953 " pdb=" N THR A 954 " pdb=" CA THR A 954 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA LEU A 697 " pdb=" C LEU A 697 " pdb=" N SER A 698 " pdb=" CA SER A 698 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 6327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1545 0.154 - 0.308: 83 0.308 - 0.461: 3 0.461 - 0.615: 3 0.615 - 0.769: 2 Chirality restraints: 1636 Sorted by residual: chirality pdb=" P DA F 1 " pdb=" OP1 DA F 1 " pdb=" OP2 DA F 1 " pdb=" O5' DA F 1 " both_signs ideal model delta sigma weight residual True 2.35 3.11 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" P DT E 25 " pdb=" OP1 DT E 25 " pdb=" OP2 DT E 25 " pdb=" O5' DT E 25 " both_signs ideal model delta sigma weight residual True 2.35 -3.01 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P DA B 6 " pdb=" OP1 DA B 6 " pdb=" OP2 DA B 6 " pdb=" O5' DA B 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.34e+00 ... (remaining 1633 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT E 27 " -0.036 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" N1 DT E 27 " 0.045 2.00e-02 2.50e+03 pdb=" C2 DT E 27 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DT E 27 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DT E 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT E 27 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT E 27 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DT E 27 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT E 27 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT E 27 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA F 1 " 0.034 2.00e-02 2.50e+03 1.85e-02 9.39e+00 pdb=" N9 DA F 1 " -0.048 2.00e-02 2.50e+03 pdb=" C8 DA F 1 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA F 1 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA F 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA F 1 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA F 1 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA F 1 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 10 " 0.033 2.00e-02 2.50e+03 1.88e-02 8.86e+00 pdb=" N1 DT B 10 " -0.046 2.00e-02 2.50e+03 pdb=" C2 DT B 10 " 0.013 2.00e-02 2.50e+03 pdb=" O2 DT B 10 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT B 10 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT B 10 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT B 10 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT B 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT B 10 " -0.004 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2908 2.86 - 3.37: 9282 3.37 - 3.88: 17119 3.88 - 4.39: 20186 4.39 - 4.90: 31188 Nonbonded interactions: 80683 Sorted by model distance: nonbonded pdb=" O PHE A 273 " pdb=" ND2 ASN A 277 " model vdw 2.353 3.120 nonbonded pdb=" O ASP A 523 " pdb=" ND2 ASN A 529 " model vdw 2.359 3.120 nonbonded pdb=" O ALA A1073 " pdb=" O MET A1076 " model vdw 2.456 3.040 nonbonded pdb=" OG1 THR A 774 " pdb=" O ASP A 776 " model vdw 2.501 3.040 nonbonded pdb=" NH1 ARG A 311 " pdb=" OD1 ASP A 315 " model vdw 2.519 3.120 ... (remaining 80678 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.140 Find NCS groups from input model: 0.100 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.007 0.066 10667 Z= 0.413 Angle : 1.150 7.832 14749 Z= 0.725 Chirality : 0.089 0.769 1636 Planarity : 0.010 0.096 1539 Dihedral : 19.146 165.375 4350 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1023 helix: -0.81 (0.17), residues: 593 sheet: 0.14 (0.71), residues: 46 loop : -0.56 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A1011 HIS 0.014 0.003 HIS A 554 PHE 0.020 0.003 PHE A 367 TYR 0.039 0.006 TYR A 914 ARG 0.017 0.003 ARG A1052 Details of bonding type rmsd hydrogen bonds : bond 0.24024 ( 549) hydrogen bonds : angle 6.82036 ( 1552) metal coordination : bond 0.01626 ( 4) metal coordination : angle 4.37063 ( 3) covalent geometry : bond 0.00748 (10663) covalent geometry : angle 1.14805 (14746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.158 Fit side-chains REVERT: A 271 LYS cc_start: 0.8494 (mttt) cc_final: 0.8238 (mtmm) REVERT: A 272 MET cc_start: 0.7557 (tpp) cc_final: 0.7306 (tpp) REVERT: A 358 LYS cc_start: 0.7812 (mttt) cc_final: 0.7314 (ttmt) REVERT: A 379 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7562 (mmm-85) REVERT: A 393 ILE cc_start: 0.7546 (pt) cc_final: 0.7306 (pp) REVERT: A 406 GLU cc_start: 0.7261 (tt0) cc_final: 0.6707 (tp30) REVERT: A 531 ARG cc_start: 0.8303 (ptt90) cc_final: 0.7767 (ppp80) REVERT: A 747 ARG cc_start: 0.6689 (mtt180) cc_final: 0.6297 (mpp-170) REVERT: A 765 ARG cc_start: 0.9030 (ptt90) cc_final: 0.8523 (ptp90) REVERT: A 776 ASP cc_start: 0.7970 (m-30) cc_final: 0.7740 (t70) REVERT: A 863 GLN cc_start: 0.8012 (tt0) cc_final: 0.7469 (tp40) REVERT: A 910 HIS cc_start: 0.7484 (m-70) cc_final: 0.6500 (p90) REVERT: A 929 ASP cc_start: 0.8160 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1011 TRP cc_start: 0.6378 (m100) cc_final: 0.6103 (m-10) REVERT: A 1047 LYS cc_start: 0.7868 (mttt) cc_final: 0.7537 (mttm) REVERT: A 1063 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7038 (tptp) REVERT: A 1064 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6902 (mtmt) REVERT: A 1066 ASN cc_start: 0.7678 (m-40) cc_final: 0.7440 (m110) REVERT: A 1082 LYS cc_start: 0.8160 (mttt) cc_final: 0.7724 (tttm) REVERT: A 1104 MET cc_start: 0.8366 (tpt) cc_final: 0.8119 (tpp) REVERT: A 1182 ASN cc_start: 0.7554 (m-40) cc_final: 0.7253 (p0) REVERT: A 1191 ASP cc_start: 0.7980 (m-30) cc_final: 0.7435 (p0) REVERT: A 1240 PHE cc_start: 0.7922 (t80) cc_final: 0.7523 (t80) REVERT: A 1267 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7266 (mmm-85) REVERT: A 1269 PHE cc_start: 0.7482 (p90) cc_final: 0.7124 (p90) outliers start: 0 outliers final: 1 residues processed: 125 average time/residue: 1.7440 time to fit residues: 230.8573 Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 309 GLN A 554 HIS A 618 ASN A 710 ASN A 851 GLN A 865 ASN A 910 HIS A1055 ASN A1077 ASN A1113 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128377 restraints weight = 12003.175| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.80 r_work: 0.3452 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10667 Z= 0.154 Angle : 0.599 6.160 14749 Z= 0.354 Chirality : 0.039 0.141 1636 Planarity : 0.004 0.043 1539 Dihedral : 21.604 177.970 2100 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.49 % Allowed : 4.14 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1023 helix: 1.65 (0.20), residues: 609 sheet: 0.40 (0.70), residues: 46 loop : 0.00 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 799 HIS 0.007 0.001 HIS A 263 PHE 0.014 0.002 PHE A 367 TYR 0.012 0.001 TYR A 260 ARG 0.006 0.001 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.05717 ( 549) hydrogen bonds : angle 4.14209 ( 1552) metal coordination : bond 0.00590 ( 4) metal coordination : angle 1.77630 ( 3) covalent geometry : bond 0.00311 (10663) covalent geometry : angle 0.59865 (14746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.189 Fit side-chains REVERT: A 272 MET cc_start: 0.7397 (tpp) cc_final: 0.7142 (tpt) REVERT: A 358 LYS cc_start: 0.7466 (mttt) cc_final: 0.7130 (ttpt) REVERT: A 379 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.7124 (mmm-85) REVERT: A 444 GLU cc_start: 0.7514 (tt0) cc_final: 0.7100 (tm-30) REVERT: A 531 ARG cc_start: 0.7993 (ptt90) cc_final: 0.7500 (ppp80) REVERT: A 765 ARG cc_start: 0.8997 (ptt90) cc_final: 0.8732 (ptp90) REVERT: A 863 GLN cc_start: 0.8008 (tt0) cc_final: 0.7661 (tp40) REVERT: A 910 HIS cc_start: 0.7083 (m90) cc_final: 0.6491 (p90) REVERT: A 1119 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: A 1162 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7003 (mtp180) REVERT: A 1191 ASP cc_start: 0.7731 (m-30) cc_final: 0.7360 (p0) REVERT: A 1267 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7741 (mmm-85) outliers start: 14 outliers final: 1 residues processed: 118 average time/residue: 1.7166 time to fit residues: 215.7394 Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.0870 chunk 86 optimal weight: 8.9990 chunk 67 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 61 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 865 ASN A1077 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130806 restraints weight = 12150.600| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.73 r_work: 0.3532 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10667 Z= 0.122 Angle : 0.488 6.147 14749 Z= 0.286 Chirality : 0.035 0.126 1636 Planarity : 0.004 0.043 1539 Dihedral : 21.322 176.057 2098 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.06 % Allowed : 7.33 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1023 helix: 2.35 (0.21), residues: 617 sheet: 0.33 (0.67), residues: 46 loop : 0.13 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1224 HIS 0.003 0.001 HIS A 585 PHE 0.013 0.001 PHE A1269 TYR 0.009 0.001 TYR A1227 ARG 0.006 0.000 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 549) hydrogen bonds : angle 3.65065 ( 1552) metal coordination : bond 0.00545 ( 4) metal coordination : angle 2.32687 ( 3) covalent geometry : bond 0.00240 (10663) covalent geometry : angle 0.48715 (14746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.054 Fit side-chains REVERT: A 272 MET cc_start: 0.7410 (tpp) cc_final: 0.7156 (tpt) REVERT: A 358 LYS cc_start: 0.7379 (mttt) cc_final: 0.7079 (ttpt) REVERT: A 418 LEU cc_start: 0.7899 (tp) cc_final: 0.7515 (tp) REVERT: A 444 GLU cc_start: 0.7363 (tt0) cc_final: 0.6964 (tm-30) REVERT: A 531 ARG cc_start: 0.7862 (ptt90) cc_final: 0.7378 (ppp80) REVERT: A 692 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7141 (ptmm) REVERT: A 863 GLN cc_start: 0.7904 (tt0) cc_final: 0.7594 (mm110) REVERT: A 910 HIS cc_start: 0.7089 (m90) cc_final: 0.6419 (p90) REVERT: A 1013 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6122 (mm) REVERT: A 1042 THR cc_start: 0.8021 (m) cc_final: 0.7776 (p) REVERT: A 1191 ASP cc_start: 0.7465 (m-30) cc_final: 0.7118 (m-30) REVERT: A 1267 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7675 (mmm-85) outliers start: 10 outliers final: 2 residues processed: 103 average time/residue: 1.5983 time to fit residues: 175.2469 Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 1013 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.177005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127921 restraints weight = 11870.624| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.77 r_work: 0.3477 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10667 Z= 0.122 Angle : 0.488 6.051 14749 Z= 0.285 Chirality : 0.036 0.131 1636 Planarity : 0.004 0.042 1539 Dihedral : 21.222 171.389 2098 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.70 % Allowed : 9.35 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.26), residues: 1023 helix: 2.43 (0.21), residues: 619 sheet: 0.24 (0.67), residues: 46 loop : 0.20 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 849 HIS 0.005 0.001 HIS A 263 PHE 0.015 0.001 PHE A1269 TYR 0.009 0.001 TYR A 731 ARG 0.006 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 549) hydrogen bonds : angle 3.63879 ( 1552) metal coordination : bond 0.00305 ( 4) metal coordination : angle 1.55215 ( 3) covalent geometry : bond 0.00244 (10663) covalent geometry : angle 0.48708 (14746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.248 Fit side-chains REVERT: A 272 MET cc_start: 0.7396 (tpp) cc_final: 0.7115 (tpt) REVERT: A 358 LYS cc_start: 0.7370 (mttt) cc_final: 0.7035 (ttpt) REVERT: A 418 LEU cc_start: 0.7922 (tp) cc_final: 0.7585 (tp) REVERT: A 434 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7151 (t70) REVERT: A 444 GLU cc_start: 0.7419 (tt0) cc_final: 0.6995 (tm-30) REVERT: A 531 ARG cc_start: 0.7935 (ptt90) cc_final: 0.7396 (ppp80) REVERT: A 692 LYS cc_start: 0.7562 (mmmt) cc_final: 0.7177 (ptmm) REVERT: A 853 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.7308 (ppt-90) REVERT: A 863 GLN cc_start: 0.7925 (tt0) cc_final: 0.7588 (mm110) REVERT: A 910 HIS cc_start: 0.7124 (m90) cc_final: 0.6421 (p90) REVERT: A 1042 THR cc_start: 0.8074 (m) cc_final: 0.7785 (p) REVERT: A 1064 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7273 (ptpt) REVERT: A 1191 ASP cc_start: 0.7596 (m-30) cc_final: 0.7224 (m-30) REVERT: A 1255 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 1267 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7687 (mmm-85) outliers start: 16 outliers final: 4 residues processed: 95 average time/residue: 1.6552 time to fit residues: 166.9734 Evaluate side-chains 88 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125106 restraints weight = 11785.265| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.72 r_work: 0.3425 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10667 Z= 0.132 Angle : 0.512 6.107 14749 Z= 0.296 Chirality : 0.037 0.133 1636 Planarity : 0.004 0.041 1539 Dihedral : 21.150 165.241 2098 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.81 % Allowed : 9.78 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.26), residues: 1023 helix: 2.38 (0.21), residues: 612 sheet: 0.29 (0.65), residues: 46 loop : 0.18 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 849 HIS 0.006 0.001 HIS A 263 PHE 0.016 0.001 PHE A1269 TYR 0.011 0.001 TYR A 731 ARG 0.003 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 549) hydrogen bonds : angle 3.72477 ( 1552) metal coordination : bond 0.00223 ( 4) metal coordination : angle 1.20728 ( 3) covalent geometry : bond 0.00274 (10663) covalent geometry : angle 0.51211 (14746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.130 Fit side-chains REVERT: A 272 MET cc_start: 0.7420 (tpp) cc_final: 0.7146 (tpt) REVERT: A 358 LYS cc_start: 0.7415 (mttt) cc_final: 0.7103 (ttpt) REVERT: A 434 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7274 (t70) REVERT: A 444 GLU cc_start: 0.7461 (tt0) cc_final: 0.7008 (tm-30) REVERT: A 531 ARG cc_start: 0.8019 (ptt90) cc_final: 0.7495 (ppp80) REVERT: A 863 GLN cc_start: 0.7945 (tt0) cc_final: 0.7627 (mm110) REVERT: A 910 HIS cc_start: 0.7132 (m90) cc_final: 0.6443 (p90) REVERT: A 1042 THR cc_start: 0.8077 (m) cc_final: 0.7759 (p) REVERT: A 1064 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7276 (pmmt) REVERT: A 1119 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: A 1162 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6977 (mtp180) REVERT: A 1191 ASP cc_start: 0.7770 (m-30) cc_final: 0.7285 (m-30) REVERT: A 1267 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7645 (mmm-85) outliers start: 17 outliers final: 5 residues processed: 93 average time/residue: 1.6515 time to fit residues: 163.4321 Evaluate side-chains 87 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.0040 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125769 restraints weight = 11879.045| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.87 r_work: 0.3432 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10667 Z= 0.128 Angle : 0.509 7.573 14749 Z= 0.292 Chirality : 0.037 0.130 1636 Planarity : 0.004 0.043 1539 Dihedral : 20.916 151.379 2098 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 10.20 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1023 helix: 2.39 (0.21), residues: 611 sheet: 0.32 (0.66), residues: 46 loop : 0.10 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 799 HIS 0.006 0.001 HIS A 263 PHE 0.018 0.001 PHE A1269 TYR 0.010 0.001 TYR A 731 ARG 0.005 0.001 ARG A 962 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 549) hydrogen bonds : angle 3.68748 ( 1552) metal coordination : bond 0.00209 ( 4) metal coordination : angle 0.92597 ( 3) covalent geometry : bond 0.00264 (10663) covalent geometry : angle 0.50857 (14746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.090 Fit side-chains REVERT: A 272 MET cc_start: 0.7426 (tpp) cc_final: 0.7169 (tpt) REVERT: A 284 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: A 358 LYS cc_start: 0.7473 (mttt) cc_final: 0.7116 (ttpt) REVERT: A 434 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7244 (t70) REVERT: A 444 GLU cc_start: 0.7338 (tt0) cc_final: 0.6873 (tm-30) REVERT: A 531 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7477 (ppp80) REVERT: A 863 GLN cc_start: 0.7976 (tt0) cc_final: 0.7633 (mm110) REVERT: A 910 HIS cc_start: 0.7142 (m90) cc_final: 0.6381 (p90) REVERT: A 1042 THR cc_start: 0.8049 (m) cc_final: 0.7711 (p) REVERT: A 1119 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7922 (mmm) REVERT: A 1162 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6945 (mtp180) REVERT: A 1191 ASP cc_start: 0.7706 (m-30) cc_final: 0.7209 (m-30) REVERT: A 1267 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7648 (mmm-85) outliers start: 18 outliers final: 5 residues processed: 95 average time/residue: 1.6070 time to fit residues: 162.6547 Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 0.5980 chunk 70 optimal weight: 0.0010 chunk 7 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 86 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.179231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130503 restraints weight = 12175.767| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.79 r_work: 0.3502 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10667 Z= 0.108 Angle : 0.465 5.986 14749 Z= 0.269 Chirality : 0.035 0.125 1636 Planarity : 0.004 0.041 1539 Dihedral : 20.689 135.376 2098 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.17 % Allowed : 11.26 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.26), residues: 1023 helix: 2.56 (0.21), residues: 608 sheet: 0.25 (0.66), residues: 46 loop : 0.21 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 799 HIS 0.004 0.001 HIS A 263 PHE 0.019 0.001 PHE A1269 TYR 0.008 0.001 TYR A1227 ARG 0.004 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 549) hydrogen bonds : angle 3.50641 ( 1552) metal coordination : bond 0.00278 ( 4) metal coordination : angle 1.14715 ( 3) covalent geometry : bond 0.00216 (10663) covalent geometry : angle 0.46510 (14746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.023 Fit side-chains REVERT: A 272 MET cc_start: 0.7376 (tpp) cc_final: 0.7102 (tpt) REVERT: A 358 LYS cc_start: 0.7359 (mttt) cc_final: 0.7018 (ttpt) REVERT: A 444 GLU cc_start: 0.7226 (tt0) cc_final: 0.6800 (tm-30) REVERT: A 531 ARG cc_start: 0.7957 (ptt90) cc_final: 0.7487 (ppp80) REVERT: A 853 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.7343 (ppt-90) REVERT: A 863 GLN cc_start: 0.7866 (tt0) cc_final: 0.7619 (mm110) REVERT: A 910 HIS cc_start: 0.7079 (m90) cc_final: 0.6361 (p90) REVERT: A 945 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7126 (mpt-90) REVERT: A 1042 THR cc_start: 0.7974 (m) cc_final: 0.7690 (p) REVERT: A 1119 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8124 (mmm) REVERT: A 1191 ASP cc_start: 0.7484 (m-30) cc_final: 0.7109 (m-30) REVERT: A 1267 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7548 (mmm-85) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 1.5081 time to fit residues: 154.4964 Evaluate side-chains 82 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.175113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125687 restraints weight = 11947.951| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.68 r_work: 0.3441 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10667 Z= 0.129 Angle : 0.508 6.343 14749 Z= 0.291 Chirality : 0.036 0.132 1636 Planarity : 0.004 0.040 1539 Dihedral : 20.780 132.166 2098 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.96 % Allowed : 13.07 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.26), residues: 1023 helix: 2.39 (0.21), residues: 606 sheet: 0.28 (0.66), residues: 46 loop : 0.15 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 799 HIS 0.006 0.001 HIS A1079 PHE 0.019 0.002 PHE A1269 TYR 0.011 0.001 TYR A 731 ARG 0.005 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 549) hydrogen bonds : angle 3.65751 ( 1552) metal coordination : bond 0.00110 ( 4) metal coordination : angle 1.02627 ( 3) covalent geometry : bond 0.00268 (10663) covalent geometry : angle 0.50734 (14746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.154 Fit side-chains REVERT: A 272 MET cc_start: 0.7366 (tpp) cc_final: 0.7116 (tpt) REVERT: A 358 LYS cc_start: 0.7486 (mttt) cc_final: 0.7144 (ttpt) REVERT: A 444 GLU cc_start: 0.7322 (tt0) cc_final: 0.6899 (tm-30) REVERT: A 531 ARG cc_start: 0.8036 (ptt90) cc_final: 0.7522 (ppp80) REVERT: A 853 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.7395 (ppt-90) REVERT: A 863 GLN cc_start: 0.7946 (tt0) cc_final: 0.7728 (mm110) REVERT: A 910 HIS cc_start: 0.7125 (m90) cc_final: 0.6400 (p90) REVERT: A 1042 THR cc_start: 0.8023 (m) cc_final: 0.7684 (p) REVERT: A 1119 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: A 1191 ASP cc_start: 0.7597 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1267 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7643 (mmm-85) outliers start: 9 outliers final: 3 residues processed: 85 average time/residue: 1.5780 time to fit residues: 144.1677 Evaluate side-chains 81 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 851 GLN A 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.173198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123578 restraints weight = 11987.879| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.78 r_work: 0.3401 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10667 Z= 0.149 Angle : 0.548 6.929 14749 Z= 0.312 Chirality : 0.038 0.133 1636 Planarity : 0.004 0.042 1539 Dihedral : 20.923 125.166 2098 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.85 % Allowed : 13.07 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.26), residues: 1023 helix: 2.21 (0.21), residues: 602 sheet: 0.37 (0.66), residues: 46 loop : 0.05 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 799 HIS 0.007 0.001 HIS A 263 PHE 0.021 0.002 PHE A1269 TYR 0.014 0.002 TYR A 731 ARG 0.005 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05826 ( 549) hydrogen bonds : angle 3.83799 ( 1552) metal coordination : bond 0.00105 ( 4) metal coordination : angle 0.69272 ( 3) covalent geometry : bond 0.00323 (10663) covalent geometry : angle 0.54791 (14746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.236 Fit side-chains REVERT: A 272 MET cc_start: 0.7412 (tpp) cc_final: 0.7124 (tpt) REVERT: A 358 LYS cc_start: 0.7516 (mttt) cc_final: 0.7125 (ttpt) REVERT: A 444 GLU cc_start: 0.7392 (tt0) cc_final: 0.6936 (tm-30) REVERT: A 531 ARG cc_start: 0.8020 (ptt90) cc_final: 0.7440 (ppp80) REVERT: A 863 GLN cc_start: 0.8027 (tt0) cc_final: 0.7669 (mm110) REVERT: A 1119 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8070 (mmm) REVERT: A 1127 ASN cc_start: 0.6964 (t0) cc_final: 0.6755 (t0) REVERT: A 1191 ASP cc_start: 0.7675 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1267 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7659 (mmm-85) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 1.6813 time to fit residues: 151.8112 Evaluate side-chains 84 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 6 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 910 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126537 restraints weight = 11951.292| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.68 r_work: 0.3415 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10667 Z= 0.124 Angle : 0.501 7.017 14749 Z= 0.288 Chirality : 0.036 0.129 1636 Planarity : 0.004 0.042 1539 Dihedral : 20.774 120.296 2098 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.64 % Allowed : 13.82 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.26), residues: 1023 helix: 2.32 (0.21), residues: 605 sheet: 0.42 (0.67), residues: 46 loop : 0.01 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 799 HIS 0.007 0.001 HIS A1079 PHE 0.022 0.001 PHE A1269 TYR 0.011 0.001 TYR A 731 ARG 0.004 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 549) hydrogen bonds : angle 3.69002 ( 1552) metal coordination : bond 0.00111 ( 4) metal coordination : angle 0.82734 ( 3) covalent geometry : bond 0.00255 (10663) covalent geometry : angle 0.50087 (14746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.997 Fit side-chains REVERT: A 272 MET cc_start: 0.7409 (tpp) cc_final: 0.7142 (tpt) REVERT: A 358 LYS cc_start: 0.7571 (mttt) cc_final: 0.7217 (ttpt) REVERT: A 444 GLU cc_start: 0.7269 (tt0) cc_final: 0.6870 (tm-30) REVERT: A 529 ASN cc_start: 0.7525 (m-40) cc_final: 0.7320 (m-40) REVERT: A 531 ARG cc_start: 0.8061 (ptt90) cc_final: 0.7545 (ppp80) REVERT: A 853 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8315 (mmm160) REVERT: A 863 GLN cc_start: 0.8080 (tt0) cc_final: 0.7737 (mm110) REVERT: A 1042 THR cc_start: 0.8105 (m) cc_final: 0.7750 (p) REVERT: A 1119 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: A 1191 ASP cc_start: 0.7699 (m-30) cc_final: 0.7220 (m-30) REVERT: A 1267 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7705 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 1.6795 time to fit residues: 149.5484 Evaluate side-chains 81 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124297 restraints weight = 11916.591| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.72 r_work: 0.3411 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10667 Z= 0.140 Angle : 0.530 7.212 14749 Z= 0.302 Chirality : 0.037 0.131 1636 Planarity : 0.004 0.042 1539 Dihedral : 20.859 114.147 2098 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.74 % Allowed : 13.50 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1023 helix: 2.21 (0.21), residues: 605 sheet: 0.42 (0.67), residues: 46 loop : -0.05 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 799 HIS 0.006 0.001 HIS A 263 PHE 0.022 0.002 PHE A1269 TYR 0.013 0.001 TYR A 731 ARG 0.005 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 549) hydrogen bonds : angle 3.78052 ( 1552) metal coordination : bond 0.00050 ( 4) metal coordination : angle 0.79849 ( 3) covalent geometry : bond 0.00299 (10663) covalent geometry : angle 0.53015 (14746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12012.92 seconds wall clock time: 209 minutes 44.77 seconds (12584.77 seconds total)