Starting phenix.real_space_refine on Wed Sep 17 18:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdq_52072/09_2025/9hdq_52072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdq_52072/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9hdq_52072/09_2025/9hdq_52072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdq_52072/09_2025/9hdq_52072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hdq_52072/09_2025/9hdq_52072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdq_52072/09_2025/9hdq_52072.map" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.43, per 1000 atoms: 0.24 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: 0.97 Conformation dependent library (CDL) restraints added in 269.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.44 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: 2.50 Time building geometry restraints manager: 1.17 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: 4.470 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.003 ARG A1052 TYR 0.039 0.006 TYR A 914 PHE 0.020 0.003 PHE A 367 TRP 0.032 0.004 TRP A1011 HIS 0.014 0.003 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00748 (10663) covalent geometry : angle 1.14805 (14746) hydrogen bonds : bond 0.24024 ( 549) hydrogen bonds : angle 6.82036 ( 1552) metal coordination : bond 0.01626 ( 4) metal coordination : angle 4.37063 ( 3) *********************** 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 : 0.324 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: 0.8167 time to fit residues: 107.7382 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 : 0.442 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.174429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126633 restraints weight = 11909.325| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.62 r_work: 0.3434 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10667 Z= 0.163 Angle : 0.614 6.170 14749 Z= 0.363 Chirality : 0.040 0.147 1636 Planarity : 0.004 0.045 1539 Dihedral : 21.652 176.972 2100 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.28 % Allowed : 4.68 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.26), residues: 1023 helix: 1.56 (0.20), residues: 608 sheet: 0.38 (0.69), residues: 46 loop : 0.01 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 522 TYR 0.011 0.001 TYR A 260 PHE 0.015 0.002 PHE A 367 TRP 0.013 0.001 TRP A1158 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00330 (10663) covalent geometry : angle 0.61339 (14746) hydrogen bonds : bond 0.06258 ( 549) hydrogen bonds : angle 4.21333 ( 1552) metal coordination : bond 0.00536 ( 4) metal coordination : angle 1.82426 ( 3) *********************** 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 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.349 Fit side-chains REVERT: A 272 MET cc_start: 0.7417 (tpp) cc_final: 0.7158 (tpt) REVERT: A 282 THR cc_start: 0.8071 (p) cc_final: 0.7845 (t) REVERT: A 358 LYS cc_start: 0.7546 (mttt) cc_final: 0.7199 (ttpt) REVERT: A 379 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.7131 (mmm-85) REVERT: A 434 ASP cc_start: 0.7721 (t70) cc_final: 0.7335 (m-30) REVERT: A 444 GLU cc_start: 0.7391 (tt0) cc_final: 0.7089 (tm-30) REVERT: A 531 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7504 (ppp80) REVERT: A 863 GLN cc_start: 0.7979 (tt0) cc_final: 0.7646 (tp40) REVERT: A 910 HIS cc_start: 0.7060 (m90) cc_final: 0.6508 (p90) REVERT: A 1104 MET cc_start: 0.8465 (tpt) cc_final: 0.8245 (tpp) REVERT: A 1162 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7041 (mtp180) REVERT: A 1191 ASP cc_start: 0.7712 (m-30) cc_final: 0.7383 (p0) REVERT: A 1267 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7771 (mmm-85) outliers start: 12 outliers final: 3 residues processed: 113 average time/residue: 0.8349 time to fit residues: 99.6397 Evaluate side-chains 90 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1016 LEU 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 65 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.174956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125922 restraints weight = 11928.240| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.74 r_work: 0.3438 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2514 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= 0.139 Angle : 0.535 6.118 14749 Z= 0.314 Chirality : 0.037 0.135 1636 Planarity : 0.004 0.047 1539 Dihedral : 21.520 178.693 2098 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.28 % Allowed : 7.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.26), residues: 1023 helix: 2.12 (0.20), residues: 609 sheet: 0.33 (0.68), residues: 46 loop : 0.24 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 522 TYR 0.010 0.001 TYR A 634 PHE 0.013 0.001 PHE A 367 TRP 0.011 0.001 TRP A 573 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00281 (10663) covalent geometry : angle 0.53452 (14746) hydrogen bonds : bond 0.05462 ( 549) hydrogen bonds : angle 3.89759 ( 1552) metal coordination : bond 0.00423 ( 4) metal coordination : angle 1.93237 ( 3) *********************** 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 111 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.500 Fit side-chains REVERT: A 272 MET cc_start: 0.7378 (tpp) cc_final: 0.7091 (tpt) REVERT: A 358 LYS cc_start: 0.7483 (mttt) cc_final: 0.7150 (ttpt) REVERT: A 379 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.7059 (mmm-85) REVERT: A 444 GLU cc_start: 0.7410 (tt0) cc_final: 0.6999 (tm-30) REVERT: A 531 ARG cc_start: 0.8020 (ptt90) cc_final: 0.7500 (ppp80) REVERT: A 863 GLN cc_start: 0.7964 (tt0) cc_final: 0.7647 (tp40) REVERT: A 910 HIS cc_start: 0.7083 (m90) cc_final: 0.6429 (p90) REVERT: A 1042 THR cc_start: 0.8038 (m) cc_final: 0.7720 (p) REVERT: A 1104 MET cc_start: 0.8439 (tpt) cc_final: 0.8221 (tpp) REVERT: A 1119 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: A 1191 ASP cc_start: 0.7753 (m-30) cc_final: 0.7341 (p0) REVERT: A 1267 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7729 (mmm-85) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.8346 time to fit residues: 92.9987 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A1077 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.176006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124994 restraints weight = 11903.388| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.72 r_work: 0.3448 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2910 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= 0.127 Angle : 0.501 6.166 14749 Z= 0.293 Chirality : 0.036 0.131 1636 Planarity : 0.004 0.046 1539 Dihedral : 21.273 177.225 2098 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.91 % Allowed : 8.40 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1023 helix: 2.33 (0.21), residues: 610 sheet: 0.31 (0.66), residues: 46 loop : 0.19 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.010 0.001 TYR A 731 PHE 0.016 0.001 PHE A1269 TRP 0.010 0.001 TRP A 573 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00259 (10663) covalent geometry : angle 0.50097 (14746) hydrogen bonds : bond 0.04811 ( 549) hydrogen bonds : angle 3.76084 ( 1552) metal coordination : bond 0.00332 ( 4) metal coordination : angle 1.63791 ( 3) *********************** 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 108 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.391 Fit side-chains REVERT: A 272 MET cc_start: 0.7447 (tpp) cc_final: 0.7152 (tpt) REVERT: A 358 LYS cc_start: 0.7358 (mttt) cc_final: 0.7064 (ttpt) REVERT: A 434 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7266 (t0) REVERT: A 444 GLU cc_start: 0.7279 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 531 ARG cc_start: 0.7999 (ptt90) cc_final: 0.7491 (ppp80) REVERT: A 863 GLN cc_start: 0.7898 (tt0) cc_final: 0.7588 (mm110) REVERT: A 910 HIS cc_start: 0.7099 (m90) cc_final: 0.6402 (p90) REVERT: A 1042 THR cc_start: 0.8068 (m) cc_final: 0.7743 (p) REVERT: A 1064 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7294 (pmmt) REVERT: A 1104 MET cc_start: 0.8388 (tpt) cc_final: 0.8151 (tpp) REVERT: A 1119 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: A 1162 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6992 (mtp180) REVERT: A 1191 ASP cc_start: 0.7585 (m-30) cc_final: 0.7225 (m-30) REVERT: A 1267 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7724 (mmm-85) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 0.7991 time to fit residues: 84.4765 Evaluate side-chains 92 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET 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 556 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 851 GLN 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 = 0.175682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125128 restraints weight = 11815.768| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.75 r_work: 0.3430 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10667 Z= 0.128 Angle : 0.503 6.114 14749 Z= 0.291 Chirality : 0.036 0.130 1636 Planarity : 0.004 0.044 1539 Dihedral : 21.173 174.268 2098 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.49 % Allowed : 9.88 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.26), residues: 1023 helix: 2.32 (0.21), residues: 611 sheet: 0.33 (0.65), residues: 46 loop : 0.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.010 0.001 TYR A 731 PHE 0.017 0.001 PHE A1269 TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00261 (10663) covalent geometry : angle 0.50288 (14746) hydrogen bonds : bond 0.04954 ( 549) hydrogen bonds : angle 3.72776 ( 1552) metal coordination : bond 0.00273 ( 4) metal coordination : angle 1.34980 ( 3) *********************** 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 102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.308 Fit side-chains REVERT: A 272 MET cc_start: 0.7466 (tpp) cc_final: 0.7196 (tpt) REVERT: A 358 LYS cc_start: 0.7437 (mttt) cc_final: 0.7080 (ttpt) REVERT: A 434 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7278 (t0) REVERT: A 444 GLU cc_start: 0.7310 (tt0) cc_final: 0.6881 (tm-30) REVERT: A 531 ARG cc_start: 0.8017 (ptt90) cc_final: 0.7497 (ppp80) REVERT: A 863 GLN cc_start: 0.7958 (tt0) cc_final: 0.7636 (mm110) REVERT: A 910 HIS cc_start: 0.7129 (m90) cc_final: 0.6409 (p90) REVERT: A 1042 THR cc_start: 0.8076 (m) cc_final: 0.7748 (p) REVERT: A 1104 MET cc_start: 0.8385 (tpt) cc_final: 0.8140 (tpp) REVERT: A 1119 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: A 1162 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6961 (mtp180) REVERT: A 1191 ASP cc_start: 0.7582 (m-30) cc_final: 0.7164 (m-30) REVERT: A 1267 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7637 (mmm-85) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 0.7958 time to fit residues: 80.8194 Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 556 LYS Chi-restraints excluded: chain A residue 862 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.175040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124726 restraints weight = 11991.570| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.78 r_work: 0.3420 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3177 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= 0.129 Angle : 0.508 6.113 14749 Z= 0.293 Chirality : 0.036 0.131 1636 Planarity : 0.004 0.042 1539 Dihedral : 20.989 169.506 2098 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.13 % Allowed : 9.67 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.26), residues: 1023 helix: 2.30 (0.21), residues: 611 sheet: 0.28 (0.65), residues: 46 loop : 0.04 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 962 TYR 0.010 0.001 TYR A 731 PHE 0.018 0.001 PHE A1269 TRP 0.014 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00267 (10663) covalent geometry : angle 0.50747 (14746) hydrogen bonds : bond 0.05032 ( 549) hydrogen bonds : angle 3.72152 ( 1552) metal coordination : bond 0.00259 ( 4) metal coordination : angle 1.16167 ( 3) *********************** 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 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.391 Fit side-chains REVERT: A 266 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6886 (mmt) REVERT: A 272 MET cc_start: 0.7460 (tpp) cc_final: 0.7162 (tpt) REVERT: A 358 LYS cc_start: 0.7505 (mttt) cc_final: 0.7137 (ttpt) REVERT: A 434 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7300 (t0) REVERT: A 444 GLU cc_start: 0.7346 (tt0) cc_final: 0.6858 (tm-30) REVERT: A 528 GLU cc_start: 0.7384 (mp0) cc_final: 0.7182 (mp0) REVERT: A 531 ARG cc_start: 0.7983 (ptt90) cc_final: 0.7464 (ppp80) REVERT: A 853 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8276 (mmm160) REVERT: A 863 GLN cc_start: 0.7978 (tt0) cc_final: 0.7671 (mm110) REVERT: A 910 HIS cc_start: 0.7090 (m90) cc_final: 0.6449 (p90) REVERT: A 1042 THR cc_start: 0.8083 (m) cc_final: 0.7751 (p) REVERT: A 1104 MET cc_start: 0.8364 (tpt) cc_final: 0.8113 (tpp) REVERT: A 1119 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: A 1162 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6948 (mtp180) REVERT: A 1191 ASP cc_start: 0.7542 (m-30) cc_final: 0.7161 (m-30) REVERT: A 1267 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7646 (mmm-85) outliers start: 20 outliers final: 7 residues processed: 99 average time/residue: 0.8053 time to fit residues: 84.4587 Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET 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 454 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.171910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122684 restraints weight = 11889.546| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.68 r_work: 0.3375 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10667 Z= 0.173 Angle : 0.580 7.319 14749 Z= 0.330 Chirality : 0.039 0.136 1636 Planarity : 0.004 0.043 1539 Dihedral : 21.167 167.876 2098 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.91 % Allowed : 10.41 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1023 helix: 2.02 (0.20), residues: 608 sheet: 0.34 (0.64), residues: 46 loop : -0.08 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 962 TYR 0.014 0.002 TYR A 634 PHE 0.019 0.002 PHE A1269 TRP 0.015 0.001 TRP A 799 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00386 (10663) covalent geometry : angle 0.57978 (14746) hydrogen bonds : bond 0.06402 ( 549) hydrogen bonds : angle 3.98371 ( 1552) metal coordination : bond 0.00259 ( 4) metal coordination : angle 0.92313 ( 3) *********************** 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 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.385 Fit side-chains REVERT: A 272 MET cc_start: 0.7404 (tpp) cc_final: 0.7131 (tpt) REVERT: A 358 LYS cc_start: 0.7587 (mttt) cc_final: 0.7228 (ttpt) REVERT: A 434 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7365 (t0) REVERT: A 444 GLU cc_start: 0.7445 (tt0) cc_final: 0.7023 (tm-30) REVERT: A 531 ARG cc_start: 0.8044 (ptt90) cc_final: 0.7514 (ppp80) REVERT: A 692 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7445 (ttpp) REVERT: A 853 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8296 (mmm160) REVERT: A 863 GLN cc_start: 0.7976 (tt0) cc_final: 0.7634 (mm110) REVERT: A 910 HIS cc_start: 0.7113 (m90) cc_final: 0.6508 (p90) REVERT: A 1042 THR cc_start: 0.8146 (m) cc_final: 0.7747 (p) REVERT: A 1104 MET cc_start: 0.8495 (tpt) cc_final: 0.8201 (tpp) REVERT: A 1162 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: A 1191 ASP cc_start: 0.7731 (m-30) cc_final: 0.7313 (p0) REVERT: A 1267 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7763 (mmm-85) outliers start: 18 outliers final: 6 residues processed: 98 average time/residue: 0.7468 time to fit residues: 77.5970 Evaluate side-chains 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 454 THR Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.174704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125933 restraints weight = 12051.385| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.58 r_work: 0.3404 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3213 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= 0.132 Angle : 0.520 6.529 14749 Z= 0.300 Chirality : 0.037 0.129 1636 Planarity : 0.004 0.044 1539 Dihedral : 20.992 164.122 2098 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 11.37 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.26), residues: 1023 helix: 2.21 (0.21), residues: 605 sheet: 0.36 (0.64), residues: 46 loop : -0.07 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.011 0.001 TYR A 731 PHE 0.021 0.001 PHE A1269 TRP 0.016 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00273 (10663) covalent geometry : angle 0.52030 (14746) hydrogen bonds : bond 0.05236 ( 549) hydrogen bonds : angle 3.79204 ( 1552) metal coordination : bond 0.00257 ( 4) metal coordination : angle 0.91511 ( 3) *********************** 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 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.388 Fit side-chains REVERT: A 272 MET cc_start: 0.7428 (tpp) cc_final: 0.7148 (tpt) REVERT: A 358 LYS cc_start: 0.7541 (mttt) cc_final: 0.7205 (ttpt) REVERT: A 434 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7330 (t0) REVERT: A 444 GLU cc_start: 0.7415 (tt0) cc_final: 0.6997 (tm-30) REVERT: A 529 ASN cc_start: 0.7582 (m-40) cc_final: 0.7359 (m-40) REVERT: A 531 ARG cc_start: 0.8039 (ptt90) cc_final: 0.7555 (ppp80) REVERT: A 853 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8274 (mmm160) REVERT: A 863 GLN cc_start: 0.7986 (tt0) cc_final: 0.7669 (mm110) REVERT: A 1042 THR cc_start: 0.8135 (m) cc_final: 0.7763 (p) REVERT: A 1104 MET cc_start: 0.8410 (tpt) cc_final: 0.8145 (tpp) REVERT: A 1119 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: A 1162 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7013 (mtp180) REVERT: A 1191 ASP cc_start: 0.7701 (m-30) cc_final: 0.7187 (m-30) REVERT: A 1267 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7763 (mmm-85) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.8003 time to fit residues: 78.7948 Evaluate side-chains 88 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 411 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.171857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122591 restraints weight = 11954.612| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.64 r_work: 0.3368 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10667 Z= 0.171 Angle : 0.581 7.963 14749 Z= 0.330 Chirality : 0.039 0.133 1636 Planarity : 0.004 0.043 1539 Dihedral : 21.171 160.670 2098 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.38 % Allowed : 12.01 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1023 helix: 1.96 (0.20), residues: 606 sheet: 0.36 (0.65), residues: 46 loop : -0.16 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 962 TYR 0.014 0.002 TYR A 731 PHE 0.021 0.002 PHE A1269 TRP 0.017 0.002 TRP A 799 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00379 (10663) covalent geometry : angle 0.58066 (14746) hydrogen bonds : bond 0.06435 ( 549) hydrogen bonds : angle 3.99580 ( 1552) metal coordination : bond 0.00182 ( 4) metal coordination : angle 0.79980 ( 3) *********************** 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 94 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.476 Fit side-chains REVERT: A 272 MET cc_start: 0.7401 (tpp) cc_final: 0.7128 (tpt) REVERT: A 358 LYS cc_start: 0.7588 (mttt) cc_final: 0.7272 (ttpt) REVERT: A 434 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7356 (t0) REVERT: A 444 GLU cc_start: 0.7473 (tt0) cc_final: 0.7069 (tm-30) REVERT: A 692 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7468 (ttpp) REVERT: A 853 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8286 (mmm160) REVERT: A 863 GLN cc_start: 0.7954 (tt0) cc_final: 0.7642 (mm110) REVERT: A 902 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7901 (p) REVERT: A 1104 MET cc_start: 0.8489 (tpt) cc_final: 0.8198 (tpp) REVERT: A 1119 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8204 (mpp) REVERT: A 1162 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7024 (mtp180) REVERT: A 1191 ASP cc_start: 0.7718 (m-30) cc_final: 0.7314 (p0) REVERT: A 1267 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7768 (mmm-85) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.7775 time to fit residues: 74.9916 Evaluate side-chains 90 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 411 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 75 optimal weight: 0.0020 overall best weight: 0.4746 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.176391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128247 restraints weight = 11911.862| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.59 r_work: 0.3435 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10667 Z= 0.118 Angle : 0.498 7.004 14749 Z= 0.287 Chirality : 0.036 0.129 1636 Planarity : 0.004 0.044 1539 Dihedral : 20.857 151.580 2098 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.28 % Allowed : 12.22 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.26), residues: 1023 helix: 2.31 (0.21), residues: 606 sheet: 0.37 (0.66), residues: 46 loop : -0.08 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 962 TYR 0.010 0.001 TYR A1227 PHE 0.024 0.001 PHE A1269 TRP 0.023 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00233 (10663) covalent geometry : angle 0.49765 (14746) hydrogen bonds : bond 0.04590 ( 549) hydrogen bonds : angle 3.68695 ( 1552) metal coordination : bond 0.00274 ( 4) metal coordination : angle 0.99826 ( 3) ********************** 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 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.398 Fit side-chains REVERT: A 272 MET cc_start: 0.7404 (tpp) cc_final: 0.7131 (tpt) REVERT: A 358 LYS cc_start: 0.7565 (mttt) cc_final: 0.7233 (ttpt) REVERT: A 444 GLU cc_start: 0.7491 (tt0) cc_final: 0.7023 (tm-30) REVERT: A 529 ASN cc_start: 0.7585 (m-40) cc_final: 0.7366 (m-40) REVERT: A 531 ARG cc_start: 0.8052 (ptt180) cc_final: 0.7554 (ppp80) REVERT: A 853 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8263 (mmm160) REVERT: A 863 GLN cc_start: 0.7972 (tt0) cc_final: 0.7656 (mm110) REVERT: A 1119 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: A 1162 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6959 (mtp180) REVERT: A 1191 ASP cc_start: 0.7571 (m-30) cc_final: 0.7165 (m-30) REVERT: A 1267 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7760 (mmm-85) outliers start: 12 outliers final: 4 residues processed: 90 average time/residue: 0.8056 time to fit residues: 76.8385 Evaluate side-chains 84 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 556 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128547 restraints weight = 12085.405| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.63 r_work: 0.3437 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10667 Z= 0.120 Angle : 0.492 6.072 14749 Z= 0.284 Chirality : 0.036 0.128 1636 Planarity : 0.004 0.042 1539 Dihedral : 20.801 133.630 2098 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.17 % Allowed : 12.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1023 helix: 2.35 (0.21), residues: 606 sheet: 0.38 (0.66), residues: 46 loop : -0.02 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.009 0.001 TYR A1227 PHE 0.023 0.001 PHE A1269 TRP 0.025 0.001 TRP A 799 HIS 0.006 0.001 HIS A1079 Details of bonding type rmsd covalent geometry : bond 0.00244 (10663) covalent geometry : angle 0.49217 (14746) hydrogen bonds : bond 0.04721 ( 549) hydrogen bonds : angle 3.65434 ( 1552) metal coordination : bond 0.00239 ( 4) metal coordination : angle 1.08146 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5622.57 seconds wall clock time: 96 minutes 5.76 seconds (5765.76 seconds total)