Starting phenix.real_space_refine on Wed Aug 5 12:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6g_62126/08_2026/9k6g_62126.map" } resolution = 3.3 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= 0.046 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 54 5.49 5 S 39 5.16 5 C 6031 2.51 5 N 1646 2.21 5 O 1849 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8525 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 984} Chain: "B" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 404 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 12} Link IDs: {'rna3p': 11} 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 7311 SG CYS A1130 35.361 76.110 95.022 1.00 90.75 S ATOM 7346 SG CYS A1134 35.833 76.219 99.037 1.00 91.12 S ATOM 7452 SG CYS A1147 37.492 72.691 96.723 1.00 80.37 S Time building chain proxies: 2.03, per 1000 atoms: 0.21 Number of scatterers: 9620 At special positions: 0 Unit cell: (89, 121, 111, 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 54 15.00 O 1849 8.00 N 1646 7.00 C 6031 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: 0.76 Conformation dependent library (CDL) restraints added in 226.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1134 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A1142 " Number of angles added : 3 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 67.4% alpha, 6.9% beta 11 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.682A pdb=" N LEU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 283 through 311 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.630A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.612A 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: 3.522A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.798A 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 509 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 553 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.614A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.710A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.194A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 737 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 785 Processing helix chain 'A' and resid 785 through 799 Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 816 through 828 removed outlier: 4.144A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.792A 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 864 through 868 Processing helix chain 'A' and resid 874 through 893 removed outlier: 4.223A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA A 887 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.609A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1007 Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1067 through 1076 Processing helix chain 'A' and resid 1081 through 1094 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.682A pdb=" N ARG A1102 " --> pdb=" O SER A1098 " (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: 3.516A 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 Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.551A pdb=" N THR A1207 " --> pdb=" O THR A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1238 Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 5.660A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 536 removed outlier: 6.223A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 536 removed outlier: 6.223A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 removed outlier: 3.783A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (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 768 489 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2520 1.34 - 1.45: 1920 1.45 - 1.57: 5331 1.57 - 1.69: 104 1.69 - 1.81: 63 Bond restraints: 9938 Sorted by residual: bond pdb=" P DC B 20 " pdb=" O5' DC B 20 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 7.93e+00 bond pdb=" C3' DT C 24 " pdb=" C2' DT C 24 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.85e+00 bond pdb=" C3' DT C 23 " pdb=" C2' DT C 23 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.50e+00 bond pdb=" C3' DT C 27 " pdb=" C2' DT C 27 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.31e+00 bond pdb=" C3' DT C 20 " pdb=" C2' DT C 20 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.31e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 13168 1.32 - 2.65: 377 2.65 - 3.97: 47 3.97 - 5.29: 19 5.29 - 6.62: 11 Bond angle restraints: 13622 Sorted by residual: angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 28 " pdb=" C4 DT C 28 " pdb=" O4 DT C 28 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C 25 " pdb=" C4 DT C 25 " pdb=" O4 DT C 25 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 29 " pdb=" C4 DT C 29 " pdb=" O4 DT C 29 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 13617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 5792 32.98 - 65.97: 239 65.97 - 98.95: 7 98.95 - 131.94: 0 131.94 - 164.92: 1 Dihedral angle restraints: 6039 sinusoidal: 2992 harmonic: 3047 Sorted by residual: dihedral pdb=" O4' U F 24 " pdb=" C1' U F 24 " pdb=" N1 U F 24 " pdb=" C2 U F 24 " ideal model delta sinusoidal sigma weight residual -160.00 -61.97 -98.03 1 1.50e+01 4.44e-03 4.86e+01 dihedral pdb=" P U F 24 " pdb=" O5' U F 24 " pdb=" C5' U F 24 " pdb=" C4' U F 24 " ideal model delta sinusoidal sigma weight residual 170.00 5.08 164.92 1 4.00e+01 6.25e-04 1.18e+01 dihedral pdb=" CB GLU A 602 " pdb=" CG GLU A 602 " pdb=" CD GLU A 602 " pdb=" OE1 GLU A 602 " ideal model delta sinusoidal sigma weight residual 0.00 82.28 -82.28 1 3.00e+01 1.11e-03 9.23e+00 ... (remaining 6036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1489 0.117 - 0.234: 20 0.234 - 0.350: 0 0.350 - 0.467: 3 0.467 - 0.584: 6 Chirality restraints: 1518 Sorted by residual: chirality pdb=" P DC B 20 " pdb=" OP1 DC B 20 " pdb=" OP2 DC B 20 " pdb=" O5' DC B 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" P U F 24 " pdb=" OP1 U F 24 " pdb=" OP2 U F 24 " pdb=" O5' U F 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" P DC B 14 " pdb=" OP1 DC B 14 " pdb=" OP2 DC B 14 " pdb=" O5' DC B 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.49e+00 ... (remaining 1515 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 998 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 999 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 999 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 999 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 954 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 955 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 802 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 803 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 803 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 803 " -0.017 5.00e-02 4.00e+02 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1543 2.77 - 3.30: 9088 3.30 - 3.83: 17180 3.83 - 4.37: 20073 4.37 - 4.90: 33020 Nonbonded interactions: 80904 Sorted by model distance: nonbonded pdb=" O SER A 508 " pdb=" ND2 ASN A 537 " model vdw 2.234 3.120 nonbonded pdb=" O LYS A1038 " pdb=" OG1 THR A1042 " model vdw 2.247 3.040 nonbonded pdb=" O ASN A 371 " pdb=" ND2 ASN A 811 " model vdw 2.250 3.120 nonbonded pdb=" OG SER A 579 " pdb=" OH TYR A 707 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG A1078 " pdb=" OD2 ASP A1171 " model vdw 2.278 3.120 ... (remaining 80899 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 11.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 0.534 9942 Z= 0.299 Angle : 0.581 15.181 13625 Z= 0.389 Chirality : 0.057 0.584 1518 Planarity : 0.003 0.033 1513 Dihedral : 14.932 164.924 4055 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.36 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.27), residues: 1026 helix: 2.21 (0.22), residues: 616 sheet: -0.49 (0.68), residues: 47 loop : 0.80 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.013 0.001 TYR A1231 PHE 0.010 0.001 PHE A1202 TRP 0.012 0.001 TRP A1036 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.25 ( 9938) covalent geometry : angle 0.56123 / 0.39 (13622) hydrogen bonds : bond 0.12020 / 8.05 ( 505) hydrogen bonds : angle 5.37794 / 3.72 ( 1451) metal coordination : bond 0.31465 / 12.91 ( 4) metal coordination : angle 10.26061 / 5.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.324 Fit side-chains REVERT: A 256 LEU cc_start: 0.8449 (tp) cc_final: 0.8195 (tt) REVERT: A 259 ASP cc_start: 0.7727 (t70) cc_final: 0.7489 (t0) REVERT: A 357 GLN cc_start: 0.6576 (tp40) cc_final: 0.6354 (tp40) REVERT: A 375 ARG cc_start: 0.7625 (tpp80) cc_final: 0.6931 (mtt-85) REVERT: A 379 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7457 (mtm110) REVERT: A 394 LYS cc_start: 0.7391 (tttt) cc_final: 0.7135 (ttpp) REVERT: A 559 ILE cc_start: 0.8197 (mm) cc_final: 0.7947 (mt) REVERT: A 649 GLU cc_start: 0.7745 (mp0) cc_final: 0.7544 (tt0) REVERT: A 686 LYS cc_start: 0.7604 (tttt) cc_final: 0.7201 (ttmt) REVERT: A 737 LYS cc_start: 0.8162 (mttt) cc_final: 0.7587 (mmtm) REVERT: A 748 GLN cc_start: 0.7734 (mp10) cc_final: 0.7262 (mp10) REVERT: A 768 TYR cc_start: 0.8172 (t80) cc_final: 0.7890 (t80) REVERT: A 772 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7911 (mm-40) REVERT: A 839 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 897 ASP cc_start: 0.7477 (m-30) cc_final: 0.6252 (p0) REVERT: A 994 PHE cc_start: 0.7840 (t80) cc_final: 0.7563 (t80) REVERT: A 1094 LYS cc_start: 0.8040 (mttm) cc_final: 0.7811 (mptt) REVERT: A 1229 MET cc_start: 0.7449 (mmp) cc_final: 0.5039 (ttp) REVERT: A 1248 MET cc_start: 0.7981 (tpp) cc_final: 0.7647 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1164 time to fit residues: 30.1508 Evaluate side-chains 99 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.194186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144346 restraints weight = 9463.919| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.73 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9942 Z= 0.168 Angle : 0.566 7.565 13625 Z= 0.302 Chirality : 0.042 0.166 1518 Planarity : 0.004 0.048 1513 Dihedral : 17.690 161.434 1800 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.66 % Favored : 98.25 % Rotamer: Outliers : 1.27 % Allowed : 6.36 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.27), residues: 1026 helix: 2.13 (0.21), residues: 619 sheet: -0.61 (0.66), residues: 47 loop : 0.74 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 962 TYR 0.018 0.002 TYR A1184 PHE 0.015 0.002 PHE A 432 TRP 0.011 0.001 TRP A1036 HIS 0.003 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9938) covalent geometry : angle 0.56406 / 0.30 (13622) hydrogen bonds : bond 0.04165 / 2.73 ( 505) hydrogen bonds : angle 4.25101 / 2.95 ( 1451) metal coordination : bond 0.03095 / 1.15 ( 4) metal coordination : angle 2.79026 / 1.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7711 (t70) cc_final: 0.7418 (t0) REVERT: A 357 GLN cc_start: 0.6575 (tp40) cc_final: 0.6154 (tp40) REVERT: A 375 ARG cc_start: 0.7443 (tpp80) cc_final: 0.6739 (mtt-85) REVERT: A 379 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.6966 (mtm110) REVERT: A 649 GLU cc_start: 0.8124 (mp0) cc_final: 0.7624 (tt0) REVERT: A 686 LYS cc_start: 0.7885 (tttt) cc_final: 0.7454 (ttmt) REVERT: A 727 LYS cc_start: 0.7835 (mttt) cc_final: 0.7635 (mtpt) REVERT: A 737 LYS cc_start: 0.7976 (mttt) cc_final: 0.7502 (mmtm) REVERT: A 748 GLN cc_start: 0.7725 (mp10) cc_final: 0.7362 (mp10) REVERT: A 772 GLN cc_start: 0.8626 (mm-40) cc_final: 0.7983 (mm-40) REVERT: A 839 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 1017 LYS cc_start: 0.6710 (tttt) cc_final: 0.5846 (tmtt) REVERT: A 1026 THR cc_start: 0.7374 (m) cc_final: 0.7129 (p) REVERT: A 1039 ILE cc_start: 0.7660 (tt) cc_final: 0.7431 (pt) REVERT: A 1051 SER cc_start: 0.7733 (t) cc_final: 0.7482 (p) REVERT: A 1094 LYS cc_start: 0.7904 (mttm) cc_final: 0.7666 (mttm) REVERT: A 1119 MET cc_start: 0.6734 (mmm) cc_final: 0.6298 (mmm) REVERT: A 1166 LEU cc_start: 0.8074 (mt) cc_final: 0.7828 (mt) REVERT: A 1184 TYR cc_start: 0.6362 (m-80) cc_final: 0.6157 (m-80) REVERT: A 1229 MET cc_start: 0.7586 (mmp) cc_final: 0.5050 (ttp) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.1088 time to fit residues: 17.3167 Evaluate side-chains 100 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 66 optimal weight: 0.0030 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.193377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143322 restraints weight = 9515.537| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.74 r_work: 0.3376 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9942 Z= 0.145 Angle : 0.519 8.016 13625 Z= 0.279 Chirality : 0.041 0.137 1518 Planarity : 0.004 0.048 1513 Dihedral : 17.634 156.090 1800 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.15 % Rotamer: Outliers : 1.70 % Allowed : 7.42 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.27), residues: 1026 helix: 2.11 (0.21), residues: 619 sheet: -0.75 (0.66), residues: 47 loop : 0.59 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 962 TYR 0.013 0.001 TYR A1112 PHE 0.011 0.001 PHE A 432 TRP 0.011 0.001 TRP A1036 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9938) covalent geometry : angle 0.51775 / 0.28 (13622) hydrogen bonds : bond 0.03757 / 2.46 ( 505) hydrogen bonds : angle 4.14923 / 2.88 ( 1451) metal coordination : bond 0.00763 / 0.30 ( 4) metal coordination : angle 2.39373 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7698 (t70) cc_final: 0.7393 (t0) REVERT: A 266 MET cc_start: 0.7773 (tpp) cc_final: 0.7441 (tpt) REVERT: A 353 GLN cc_start: 0.5991 (tm-30) cc_final: 0.5151 (tm-30) REVERT: A 357 GLN cc_start: 0.6620 (tp40) cc_final: 0.6175 (tp40) REVERT: A 375 ARG cc_start: 0.7457 (tpp80) cc_final: 0.6720 (mtt-85) REVERT: A 379 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.6823 (mtm110) REVERT: A 394 LYS cc_start: 0.6892 (tttt) cc_final: 0.6679 (ttpp) REVERT: A 649 GLU cc_start: 0.8142 (mp0) cc_final: 0.7645 (tt0) REVERT: A 686 LYS cc_start: 0.7911 (tttt) cc_final: 0.7463 (ttmt) REVERT: A 737 LYS cc_start: 0.7944 (mttt) cc_final: 0.7467 (mmtm) REVERT: A 748 GLN cc_start: 0.7734 (mp10) cc_final: 0.7371 (mp10) REVERT: A 839 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 908 MET cc_start: 0.8275 (mpp) cc_final: 0.7366 (mpp) REVERT: A 1017 LYS cc_start: 0.6672 (tttt) cc_final: 0.5982 (tmtt) REVERT: A 1026 THR cc_start: 0.7378 (m) cc_final: 0.7123 (p) REVERT: A 1039 ILE cc_start: 0.7636 (tt) cc_final: 0.7424 (pt) REVERT: A 1051 SER cc_start: 0.7771 (t) cc_final: 0.7510 (p) REVERT: A 1166 LEU cc_start: 0.8027 (mt) cc_final: 0.7791 (mt) REVERT: A 1229 MET cc_start: 0.7566 (mmp) cc_final: 0.5045 (ttp) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.1099 time to fit residues: 16.0502 Evaluate side-chains 98 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.192863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141836 restraints weight = 9494.836| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.80 r_work: 0.3368 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9942 Z= 0.143 Angle : 0.504 8.008 13625 Z= 0.272 Chirality : 0.040 0.142 1518 Planarity : 0.004 0.046 1513 Dihedral : 17.593 152.363 1800 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.70 % Allowed : 8.27 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1026 helix: 2.04 (0.21), residues: 619 sheet: -0.82 (0.65), residues: 47 loop : 0.55 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.018 0.002 TYR A1043 PHE 0.034 0.002 PHE A 994 TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9938) covalent geometry : angle 0.50323 / 0.27 (13622) hydrogen bonds : bond 0.03611 / 2.36 ( 505) hydrogen bonds : angle 4.08169 / 2.83 ( 1451) metal coordination : bond 0.01103 / 0.42 ( 4) metal coordination : angle 2.30859 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7636 (t70) cc_final: 0.7304 (t0) REVERT: A 353 GLN cc_start: 0.5921 (tm-30) cc_final: 0.5316 (tm-30) REVERT: A 357 GLN cc_start: 0.6548 (tp40) cc_final: 0.6285 (tp40) REVERT: A 375 ARG cc_start: 0.7327 (tpp80) cc_final: 0.6568 (mtt-85) REVERT: A 379 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6852 (mtm110) REVERT: A 483 ARG cc_start: 0.8321 (mtp180) cc_final: 0.7966 (mtp180) REVERT: A 649 GLU cc_start: 0.8145 (mp0) cc_final: 0.7590 (tt0) REVERT: A 654 LYS cc_start: 0.7774 (mttt) cc_final: 0.7319 (mmtp) REVERT: A 686 LYS cc_start: 0.7928 (tttt) cc_final: 0.7353 (ttmt) REVERT: A 737 LYS cc_start: 0.7819 (mttt) cc_final: 0.7324 (mmtm) REVERT: A 748 GLN cc_start: 0.7734 (mp10) cc_final: 0.7349 (mp10) REVERT: A 839 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6978 (mm-30) REVERT: A 1017 LYS cc_start: 0.6769 (tttt) cc_final: 0.6009 (tmtt) REVERT: A 1026 THR cc_start: 0.7349 (m) cc_final: 0.7083 (p) REVERT: A 1121 ILE cc_start: 0.7221 (tt) cc_final: 0.6885 (pt) REVERT: A 1166 LEU cc_start: 0.7999 (mt) cc_final: 0.7749 (mp) REVERT: A 1189 TYR cc_start: 0.6014 (p90) cc_final: 0.4268 (m-80) REVERT: A 1229 MET cc_start: 0.7550 (mmp) cc_final: 0.5050 (ttp) REVERT: A 1248 MET cc_start: 0.7381 (tpt) cc_final: 0.6921 (tpt) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1084 time to fit residues: 15.5708 Evaluate side-chains 94 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.0060 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 13 optimal weight: 0.0060 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.1228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A1059 GLN A1127 ASN A1209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.196189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145600 restraints weight = 9514.014| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.83 r_work: 0.3409 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9942 Z= 0.102 Angle : 0.471 7.893 13625 Z= 0.257 Chirality : 0.039 0.197 1518 Planarity : 0.003 0.044 1513 Dihedral : 17.573 148.041 1800 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.85 % Allowed : 10.18 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.27), residues: 1026 helix: 2.13 (0.21), residues: 619 sheet: -0.77 (0.67), residues: 47 loop : 0.55 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1129 TYR 0.010 0.001 TYR A1232 PHE 0.009 0.001 PHE A 651 TRP 0.011 0.001 TRP A1224 HIS 0.002 0.000 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 9938) covalent geometry : angle 0.47051 / 0.26 (13622) hydrogen bonds : bond 0.03367 / 2.21 ( 505) hydrogen bonds : angle 3.96526 / 2.74 ( 1451) metal coordination : bond 0.00821 / 0.31 ( 4) metal coordination : angle 1.86374 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.216 Fit side-chains REVERT: A 259 ASP cc_start: 0.7662 (t70) cc_final: 0.7325 (t0) REVERT: A 266 MET cc_start: 0.7592 (tpp) cc_final: 0.7114 (tpt) REVERT: A 353 GLN cc_start: 0.6002 (tm-30) cc_final: 0.5371 (tm-30) REVERT: A 357 GLN cc_start: 0.6598 (tp40) cc_final: 0.6307 (tp40) REVERT: A 375 ARG cc_start: 0.7264 (tpp80) cc_final: 0.6517 (mtt-85) REVERT: A 379 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.6778 (mtm110) REVERT: A 483 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7872 (mtp180) REVERT: A 636 LYS cc_start: 0.7415 (mtmm) cc_final: 0.6745 (tttm) REVERT: A 649 GLU cc_start: 0.8147 (mp0) cc_final: 0.7559 (tt0) REVERT: A 654 LYS cc_start: 0.7742 (mttt) cc_final: 0.7287 (mmtp) REVERT: A 686 LYS cc_start: 0.7859 (tttt) cc_final: 0.7387 (ttmt) REVERT: A 737 LYS cc_start: 0.7812 (mttt) cc_final: 0.7317 (mmtm) REVERT: A 748 GLN cc_start: 0.7754 (mp10) cc_final: 0.7266 (mp10) REVERT: A 772 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7812 (mm-40) REVERT: A 839 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 1017 LYS cc_start: 0.6721 (tttt) cc_final: 0.6040 (tmtt) REVERT: A 1026 THR cc_start: 0.7302 (m) cc_final: 0.7051 (p) REVERT: A 1121 ILE cc_start: 0.7178 (tt) cc_final: 0.6803 (pt) REVERT: A 1166 LEU cc_start: 0.7944 (mt) cc_final: 0.7718 (mt) REVERT: A 1229 MET cc_start: 0.7416 (mmp) cc_final: 0.4898 (ttp) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.1106 time to fit residues: 14.5977 Evaluate side-chains 92 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.192775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141562 restraints weight = 9536.390| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.82 r_work: 0.3341 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9942 Z= 0.142 Angle : 0.499 7.884 13625 Z= 0.267 Chirality : 0.040 0.170 1518 Planarity : 0.004 0.043 1513 Dihedral : 17.584 146.103 1800 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.59 % Allowed : 10.18 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1026 helix: 2.05 (0.21), residues: 619 sheet: -0.82 (0.68), residues: 47 loop : 0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1052 TYR 0.013 0.001 TYR A1112 PHE 0.022 0.002 PHE A 994 TRP 0.008 0.001 TRP A1219 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9938) covalent geometry : angle 0.49782 / 0.27 (13622) hydrogen bonds : bond 0.03513 / 2.33 ( 505) hydrogen bonds : angle 3.98548 / 2.76 ( 1451) metal coordination : bond 0.00988 / 0.38 ( 4) metal coordination : angle 2.22784 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.355 Fit side-chains REVERT: A 259 ASP cc_start: 0.7633 (t70) cc_final: 0.7289 (t0) REVERT: A 353 GLN cc_start: 0.6008 (tm-30) cc_final: 0.5339 (tm-30) REVERT: A 357 GLN cc_start: 0.6633 (tp40) cc_final: 0.6304 (tp40) REVERT: A 375 ARG cc_start: 0.7297 (tpp80) cc_final: 0.5814 (ttp-170) REVERT: A 379 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.6677 (mtp-110) REVERT: A 636 LYS cc_start: 0.7382 (mtmm) cc_final: 0.7050 (ptpp) REVERT: A 649 GLU cc_start: 0.8108 (mp0) cc_final: 0.7490 (tt0) REVERT: A 654 LYS cc_start: 0.7806 (mttt) cc_final: 0.7367 (mmtp) REVERT: A 686 LYS cc_start: 0.7908 (tttt) cc_final: 0.7416 (ttmt) REVERT: A 737 LYS cc_start: 0.7822 (mttt) cc_final: 0.7299 (mmtm) REVERT: A 748 GLN cc_start: 0.7883 (mp10) cc_final: 0.7398 (mp10) REVERT: A 772 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7856 (mm-40) REVERT: A 945 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6418 (mtt-85) REVERT: A 1017 LYS cc_start: 0.6778 (tttt) cc_final: 0.5968 (tmtt) REVERT: A 1026 THR cc_start: 0.7352 (m) cc_final: 0.7073 (p) REVERT: A 1189 TYR cc_start: 0.6009 (p90) cc_final: 0.4337 (m-80) REVERT: A 1229 MET cc_start: 0.7521 (mmp) cc_final: 0.4951 (ttp) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 0.1292 time to fit residues: 18.0607 Evaluate side-chains 99 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1059 GLN A1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.191939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140901 restraints weight = 9571.161| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.80 r_work: 0.3349 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9942 Z= 0.129 Angle : 0.491 7.206 13625 Z= 0.263 Chirality : 0.039 0.192 1518 Planarity : 0.004 0.042 1513 Dihedral : 17.562 144.620 1800 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.70 % Allowed : 11.03 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 1026 helix: 2.04 (0.21), residues: 619 sheet: -0.86 (0.69), residues: 47 loop : 0.48 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1129 TYR 0.019 0.001 TYR A 768 PHE 0.011 0.001 PHE A 432 TRP 0.008 0.001 TRP A1158 HIS 0.002 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9938) covalent geometry : angle 0.49049 / 0.26 (13622) hydrogen bonds : bond 0.03446 / 2.28 ( 505) hydrogen bonds : angle 3.97065 / 2.75 ( 1451) metal coordination : bond 0.00976 / 0.37 ( 4) metal coordination : angle 1.97056 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.290 Fit side-chains REVERT: A 259 ASP cc_start: 0.7683 (t70) cc_final: 0.7341 (t0) REVERT: A 266 MET cc_start: 0.7669 (tpp) cc_final: 0.7428 (mmm) REVERT: A 353 GLN cc_start: 0.6035 (tm-30) cc_final: 0.5358 (tm-30) REVERT: A 357 GLN cc_start: 0.6689 (tp40) cc_final: 0.6339 (tp40) REVERT: A 375 ARG cc_start: 0.7288 (tpp80) cc_final: 0.5860 (ttp-170) REVERT: A 379 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.6700 (mtp-110) REVERT: A 636 LYS cc_start: 0.7371 (mtmm) cc_final: 0.7079 (ptpp) REVERT: A 649 GLU cc_start: 0.8086 (mp0) cc_final: 0.7522 (tt0) REVERT: A 654 LYS cc_start: 0.7858 (mttt) cc_final: 0.7448 (mmtp) REVERT: A 686 LYS cc_start: 0.7974 (tttt) cc_final: 0.7392 (ttmt) REVERT: A 737 LYS cc_start: 0.7953 (mttt) cc_final: 0.7448 (mmtm) REVERT: A 748 GLN cc_start: 0.7854 (mp10) cc_final: 0.7360 (mp10) REVERT: A 772 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8129 (mm-40) REVERT: A 945 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6544 (mtt-85) REVERT: A 1017 LYS cc_start: 0.6927 (tttt) cc_final: 0.6166 (tmtt) REVERT: A 1026 THR cc_start: 0.7438 (m) cc_final: 0.7161 (p) REVERT: A 1129 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7333 (mmp80) REVERT: A 1166 LEU cc_start: 0.7314 (mt) cc_final: 0.6432 (mp) REVERT: A 1189 TYR cc_start: 0.6073 (p90) cc_final: 0.4382 (m-80) REVERT: A 1229 MET cc_start: 0.7609 (mmp) cc_final: 0.5102 (ttp) REVERT: A 1248 MET cc_start: 0.7442 (tpt) cc_final: 0.6982 (tpt) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.1181 time to fit residues: 16.4898 Evaluate side-chains 100 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 ASN A1059 GLN A1127 ASN A1260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.188947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137791 restraints weight = 9602.563| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.76 r_work: 0.3298 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9942 Z= 0.162 Angle : 0.518 5.586 13625 Z= 0.278 Chirality : 0.041 0.190 1518 Planarity : 0.004 0.042 1513 Dihedral : 17.565 144.291 1800 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 11.03 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.27), residues: 1026 helix: 1.90 (0.21), residues: 619 sheet: -0.98 (0.70), residues: 47 loop : 0.39 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1052 TYR 0.019 0.002 TYR A 768 PHE 0.032 0.002 PHE A 994 TRP 0.008 0.001 TRP A 573 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 9938) covalent geometry : angle 0.51671 / 0.28 (13622) hydrogen bonds : bond 0.03617 / 2.41 ( 505) hydrogen bonds : angle 4.06540 / 2.83 ( 1451) metal coordination : bond 0.00989 / 0.38 ( 4) metal coordination : angle 2.13879 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.365 Fit side-chains REVERT: A 259 ASP cc_start: 0.7687 (t70) cc_final: 0.7341 (t0) REVERT: A 266 MET cc_start: 0.7729 (tpp) cc_final: 0.7431 (mmm) REVERT: A 353 GLN cc_start: 0.6079 (tm-30) cc_final: 0.5407 (tm-30) REVERT: A 357 GLN cc_start: 0.6731 (tp40) cc_final: 0.6367 (tp40) REVERT: A 375 ARG cc_start: 0.7276 (tpp80) cc_final: 0.6525 (mtt-85) REVERT: A 379 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.6742 (mtm110) REVERT: A 526 LYS cc_start: 0.5882 (mttp) cc_final: 0.5371 (mtpt) REVERT: A 636 LYS cc_start: 0.7392 (mtmm) cc_final: 0.7124 (ptpp) REVERT: A 649 GLU cc_start: 0.8128 (mp0) cc_final: 0.7538 (tt0) REVERT: A 654 LYS cc_start: 0.7869 (mttt) cc_final: 0.7464 (mmtp) REVERT: A 686 LYS cc_start: 0.8096 (tttt) cc_final: 0.7460 (ttmt) REVERT: A 737 LYS cc_start: 0.7942 (mttt) cc_final: 0.7449 (mmtm) REVERT: A 748 GLN cc_start: 0.7881 (mp10) cc_final: 0.7511 (mp10) REVERT: A 772 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8156 (mm-40) REVERT: A 945 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6530 (mtt-85) REVERT: A 1017 LYS cc_start: 0.6994 (tttt) cc_final: 0.6222 (tmtt) REVERT: A 1026 THR cc_start: 0.7488 (m) cc_final: 0.7199 (p) REVERT: A 1166 LEU cc_start: 0.7383 (mt) cc_final: 0.6634 (mp) REVERT: A 1189 TYR cc_start: 0.6089 (p90) cc_final: 0.4411 (m-80) REVERT: A 1229 MET cc_start: 0.7703 (mmp) cc_final: 0.5142 (ttp) REVERT: A 1248 MET cc_start: 0.7444 (tpt) cc_final: 0.6990 (tpt) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.1081 time to fit residues: 15.7667 Evaluate side-chains 106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 40.0000 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 ASN A1059 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143299 restraints weight = 9660.035| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.95 r_work: 0.3454 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9942 Z= 0.148 Angle : 0.511 8.240 13625 Z= 0.276 Chirality : 0.040 0.200 1518 Planarity : 0.004 0.041 1513 Dihedral : 17.554 143.632 1800 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 11.03 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1026 helix: 1.93 (0.21), residues: 614 sheet: -1.11 (0.70), residues: 47 loop : 0.40 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1052 TYR 0.018 0.001 TYR A 768 PHE 0.024 0.002 PHE A 994 TRP 0.008 0.001 TRP A1158 HIS 0.002 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9938) covalent geometry : angle 0.51060 / 0.28 (13622) hydrogen bonds : bond 0.03561 / 2.36 ( 505) hydrogen bonds : angle 4.05249 / 2.82 ( 1451) metal coordination : bond 0.01064 / 0.41 ( 4) metal coordination : angle 2.09486 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.287 Fit side-chains REVERT: A 259 ASP cc_start: 0.7817 (t70) cc_final: 0.7543 (t0) REVERT: A 266 MET cc_start: 0.8007 (tpp) cc_final: 0.7683 (mmm) REVERT: A 353 GLN cc_start: 0.6246 (tm-30) cc_final: 0.5538 (tm-30) REVERT: A 357 GLN cc_start: 0.7040 (tp40) cc_final: 0.6670 (tp40) REVERT: A 375 ARG cc_start: 0.7555 (tpp80) cc_final: 0.6804 (mtt-85) REVERT: A 379 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.6991 (mtm110) REVERT: A 526 LYS cc_start: 0.6051 (mttp) cc_final: 0.5504 (mtpt) REVERT: A 649 GLU cc_start: 0.8057 (mp0) cc_final: 0.7737 (tt0) REVERT: A 654 LYS cc_start: 0.8038 (mttt) cc_final: 0.7754 (mmtp) REVERT: A 686 LYS cc_start: 0.8267 (tttt) cc_final: 0.7708 (ttmt) REVERT: A 737 LYS cc_start: 0.8081 (mttt) cc_final: 0.7689 (mmtm) REVERT: A 748 GLN cc_start: 0.7802 (mp10) cc_final: 0.7548 (mp10) REVERT: A 772 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7944 (mm-40) REVERT: A 928 LYS cc_start: 0.7715 (tttm) cc_final: 0.7503 (mttm) REVERT: A 945 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6813 (mtt-85) REVERT: A 1017 LYS cc_start: 0.7222 (tttt) cc_final: 0.6528 (tmtt) REVERT: A 1026 THR cc_start: 0.7823 (m) cc_final: 0.7592 (p) REVERT: A 1166 LEU cc_start: 0.7497 (mt) cc_final: 0.6899 (mp) REVERT: A 1189 TYR cc_start: 0.6431 (p90) cc_final: 0.4885 (m-80) REVERT: A 1229 MET cc_start: 0.7919 (mmp) cc_final: 0.5496 (ttt) REVERT: A 1248 MET cc_start: 0.7653 (tpt) cc_final: 0.7257 (tpt) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1267 time to fit residues: 17.2485 Evaluate side-chains 106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1127 ASN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1235 ILE 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 4 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 ASN A1059 GLN A1127 ASN A1209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144163 restraints weight = 9825.256| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.01 r_work: 0.3446 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9942 Z= 0.156 Angle : 0.511 6.702 13625 Z= 0.277 Chirality : 0.040 0.211 1518 Planarity : 0.004 0.041 1513 Dihedral : 17.554 143.172 1800 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 11.13 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1026 helix: 1.93 (0.21), residues: 613 sheet: -1.10 (0.72), residues: 47 loop : 0.42 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1052 TYR 0.018 0.002 TYR A 768 PHE 0.025 0.002 PHE A 994 TRP 0.008 0.001 TRP A1036 HIS 0.003 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9938) covalent geometry : angle 0.50967 / 0.28 (13622) hydrogen bonds : bond 0.03561 / 2.36 ( 505) hydrogen bonds : angle 4.05931 / 2.83 ( 1451) metal coordination : bond 0.01022 / 0.40 ( 4) metal coordination : angle 2.13216 / 1.16 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.344 Fit side-chains REVERT: A 259 ASP cc_start: 0.7806 (t70) cc_final: 0.7534 (t0) REVERT: A 266 MET cc_start: 0.8016 (tpp) cc_final: 0.7711 (mmm) REVERT: A 353 GLN cc_start: 0.6276 (tm-30) cc_final: 0.5737 (tm-30) REVERT: A 357 GLN cc_start: 0.7062 (tp40) cc_final: 0.6708 (tp40) REVERT: A 375 ARG cc_start: 0.7539 (tpp80) cc_final: 0.6807 (mtt-85) REVERT: A 379 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.6994 (mtm110) REVERT: A 526 LYS cc_start: 0.6089 (mttp) cc_final: 0.5561 (mtpt) REVERT: A 649 GLU cc_start: 0.8089 (mp0) cc_final: 0.7751 (tt0) REVERT: A 654 LYS cc_start: 0.8039 (mttt) cc_final: 0.7728 (mmtt) REVERT: A 686 LYS cc_start: 0.8262 (tttt) cc_final: 0.7704 (ttmt) REVERT: A 737 LYS cc_start: 0.8087 (mttt) cc_final: 0.7695 (mmtm) REVERT: A 748 GLN cc_start: 0.7789 (mp10) cc_final: 0.7524 (mp10) REVERT: A 772 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7950 (mm-40) REVERT: A 928 LYS cc_start: 0.7752 (tttm) cc_final: 0.7520 (mtpt) REVERT: A 945 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6821 (mtt-85) REVERT: A 1017 LYS cc_start: 0.7260 (tttt) cc_final: 0.6587 (tmtt) REVERT: A 1026 THR cc_start: 0.7844 (m) cc_final: 0.7603 (p) REVERT: A 1166 LEU cc_start: 0.7507 (mt) cc_final: 0.6921 (mp) REVERT: A 1189 TYR cc_start: 0.6447 (p90) cc_final: 0.4888 (m-80) REVERT: A 1229 MET cc_start: 0.7938 (mmp) cc_final: 0.5518 (ttt) REVERT: A 1248 MET cc_start: 0.7656 (tpt) cc_final: 0.7262 (tpt) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.1226 time to fit residues: 16.6042 Evaluate side-chains 105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1079 HIS Chi-restraints excluded: chain A residue 1127 ASN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 77 optimal weight: 0.0020 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 ASN A1059 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144014 restraints weight = 9751.146| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.11 r_work: 0.3446 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9942 Z= 0.121 Angle : 0.490 6.181 13625 Z= 0.269 Chirality : 0.039 0.199 1518 Planarity : 0.004 0.040 1513 Dihedral : 17.549 142.562 1800 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 11.24 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 1026 helix: 2.00 (0.21), residues: 613 sheet: -1.08 (0.72), residues: 47 loop : 0.43 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1052 TYR 0.016 0.001 TYR A 768 PHE 0.023 0.002 PHE A 994 TRP 0.010 0.001 TRP A1036 HIS 0.002 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9938) covalent geometry : angle 0.48946 / 0.27 (13622) hydrogen bonds : bond 0.03488 / 2.31 ( 505) hydrogen bonds : angle 4.01227 / 2.79 ( 1451) metal coordination : bond 0.00908 / 0.34 ( 4) metal coordination : angle 2.20364 / 1.20 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.69 seconds wall clock time: 42 minutes 7.03 seconds (2527.03 seconds total)