Starting phenix.real_space_refine on Thu Jul 2 19:33:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6g_62126/07_2026/9k6g_62126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6g_62126/07_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_62126/07_2026/9k6g_62126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6g_62126/07_2026/9k6g_62126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6g_62126/07_2026/9k6g_62126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6g_62126/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.08, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 274.7 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: 1.27 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: 2.49 Time building geometry restraints manager: 1.11 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: 13188 1.32 - 2.65: 356 2.65 - 3.97: 48 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: 1496 0.117 - 0.234: 13 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: 6.020 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 13.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- 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= 0.297 Angle : 0.575 15.181 13625 Z= 0.384 Chirality : 0.056 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 0.00333 / 0.25 ( 9938) covalent geometry : angle 0.55413 / 0.38 (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 : 0.371 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: 0.6353 (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: 0.7458 (mtm110) REVERT: A 394 LYS cc_start: 0.7391 (tttt) cc_final: 0.7136 (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: 0.7812 (mptt) REVERT: A 1229 MET cc_start: 0.7449 (mmp) cc_final: 0.5040 (ttp) REVERT: A 1248 MET cc_start: 0.7981 (tpp) cc_final: 0.7648 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1294 time to fit residues: 33.3770 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 : 0.343 ------------------------------------------------------------------------------- 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: 5.9990 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 ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.192788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142587 restraints weight = 9522.454| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.76 r_work: 0.3384 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9942 Z= 0.171 Angle : 0.576 8.043 13625 Z= 0.308 Chirality : 0.043 0.163 1518 Planarity : 0.004 0.051 1513 Dihedral : 17.783 161.646 1800 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.15 % Rotamer: Outliers : 1.38 % Allowed : 6.26 % 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: 2.19 (0.27), residues: 1026 helix: 2.10 (0.21), residues: 619 sheet: -0.62 (0.66), residues: 47 loop : 0.73 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 962 TYR 0.019 0.002 TYR A1184 PHE 0.016 0.002 PHE A 432 TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9938) covalent geometry : angle 0.57504 / 0.31 (13622) hydrogen bonds : bond 0.04151 / 2.71 ( 505) hydrogen bonds : angle 4.25602 / 2.96 ( 1451) metal coordination : bond 0.02540 / 0.95 ( 4) metal coordination : angle 2.51042 / 1.25 ( 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 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7705 (t70) cc_final: 0.7410 (t0) REVERT: A 357 GLN cc_start: 0.6591 (tp40) cc_final: 0.6160 (tp40) REVERT: A 375 ARG cc_start: 0.7442 (tpp80) cc_final: 0.6715 (mtt-85) REVERT: A 379 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6873 (mtm110) REVERT: A 649 GLU cc_start: 0.8123 (mp0) cc_final: 0.7617 (tt0) REVERT: A 686 LYS cc_start: 0.7877 (tttt) cc_final: 0.7442 (ttmt) REVERT: A 727 LYS cc_start: 0.7828 (mttt) cc_final: 0.7626 (mtpt) REVERT: A 737 LYS cc_start: 0.7993 (mttt) cc_final: 0.7505 (mmtm) REVERT: A 748 GLN cc_start: 0.7719 (mp10) cc_final: 0.7355 (mp10) REVERT: A 772 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7957 (mm-40) REVERT: A 839 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 908 MET cc_start: 0.8198 (mpp) cc_final: 0.7358 (mpp) REVERT: A 1017 LYS cc_start: 0.6689 (tttt) cc_final: 0.5818 (tmtt) REVERT: A 1026 THR cc_start: 0.7366 (m) cc_final: 0.7122 (p) REVERT: A 1039 ILE cc_start: 0.7650 (tt) cc_final: 0.7428 (pt) REVERT: A 1051 SER cc_start: 0.7721 (t) cc_final: 0.7464 (p) REVERT: A 1094 LYS cc_start: 0.7893 (mttm) cc_final: 0.7654 (mttm) REVERT: A 1166 LEU cc_start: 0.8143 (mt) cc_final: 0.7913 (mt) REVERT: A 1229 MET cc_start: 0.7588 (mmp) cc_final: 0.5043 (ttp) REVERT: A 1248 MET cc_start: 0.8003 (tpp) cc_final: 0.7746 (tpt) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.1037 time to fit residues: 16.6861 Evaluate side-chains 98 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.9990 chunk 90 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** 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 = 0.4114 r_free = 0.4114 target = 0.192078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141561 restraints weight = 9543.327| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.75 r_work: 0.3351 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9942 Z= 0.169 Angle : 0.532 8.922 13625 Z= 0.285 Chirality : 0.041 0.142 1518 Planarity : 0.004 0.048 1513 Dihedral : 17.728 156.367 1800 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.15 % Rotamer: Outliers : 1.48 % Allowed : 7.53 % Favored : 90.99 % 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: 2.01 (0.27), residues: 1026 helix: 2.02 (0.21), residues: 619 sheet: -0.80 (0.65), residues: 47 loop : 0.55 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1129 TYR 0.014 0.001 TYR A1112 PHE 0.015 0.002 PHE A 994 TRP 0.010 0.001 TRP A1036 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9938) covalent geometry : angle 0.53064 / 0.29 (13622) hydrogen bonds : bond 0.03805 / 2.50 ( 505) hydrogen bonds : angle 4.19472 / 2.92 ( 1451) metal coordination : bond 0.00812 / 0.31 ( 4) metal coordination : angle 2.57347 / 1.36 ( 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 116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.338 Fit side-chains REVERT: A 259 ASP cc_start: 0.7696 (t70) cc_final: 0.7388 (t0) REVERT: A 353 GLN cc_start: 0.5975 (tm-30) cc_final: 0.5129 (tm-30) REVERT: A 357 GLN cc_start: 0.6606 (tp40) cc_final: 0.6156 (tp40) REVERT: A 375 ARG cc_start: 0.7368 (tpp80) cc_final: 0.6611 (mtt-85) REVERT: A 379 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.6903 (mtm110) REVERT: A 394 LYS cc_start: 0.6879 (tttt) cc_final: 0.6673 (ttpp) REVERT: A 526 LYS cc_start: 0.5681 (mttp) cc_final: 0.5193 (mtpt) REVERT: A 649 GLU cc_start: 0.8105 (mp0) cc_final: 0.7631 (tt0) REVERT: A 686 LYS cc_start: 0.7943 (tttt) cc_final: 0.7386 (ttmt) REVERT: A 737 LYS cc_start: 0.7877 (mttt) cc_final: 0.7385 (mmtm) REVERT: A 748 GLN cc_start: 0.7743 (mp10) cc_final: 0.7378 (mp10) REVERT: A 772 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7923 (mm-40) REVERT: A 839 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 945 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6564 (mtt-85) REVERT: A 1017 LYS cc_start: 0.6595 (tttt) cc_final: 0.5945 (tmtt) REVERT: A 1026 THR cc_start: 0.7390 (m) cc_final: 0.7112 (p) REVERT: A 1039 ILE cc_start: 0.7672 (tt) cc_final: 0.7469 (pt) REVERT: A 1051 SER cc_start: 0.7802 (t) cc_final: 0.7516 (p) REVERT: A 1121 ILE cc_start: 0.7199 (tt) cc_final: 0.6862 (pt) REVERT: A 1166 LEU cc_start: 0.8018 (mt) cc_final: 0.7805 (mt) REVERT: A 1180 TYR cc_start: 0.8086 (m-80) cc_final: 0.7797 (m-80) REVERT: A 1189 TYR cc_start: 0.6167 (p90) cc_final: 0.4520 (m-80) REVERT: A 1229 MET cc_start: 0.7615 (mmp) cc_final: 0.5054 (ttp) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.1205 time to fit residues: 18.1284 Evaluate side-chains 106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 640 ASN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 VAL 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: 0.3980 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** 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 = 0.4101 r_free = 0.4101 target = 0.190925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140306 restraints weight = 9515.039| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.78 r_work: 0.3353 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9942 Z= 0.139 Angle : 0.499 9.244 13625 Z= 0.270 Chirality : 0.040 0.143 1518 Planarity : 0.004 0.047 1513 Dihedral : 17.689 153.741 1800 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.70 % Allowed : 8.06 % Favored : 90.24 % 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: 2.01 (0.21), residues: 619 sheet: -0.89 (0.65), residues: 47 loop : 0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1052 TYR 0.017 0.001 TYR A1043 PHE 0.011 0.001 PHE A 432 TRP 0.011 0.001 TRP A1036 HIS 0.002 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9938) covalent geometry : angle 0.49770 / 0.27 (13622) hydrogen bonds : bond 0.03612 / 2.37 ( 505) hydrogen bonds : angle 4.10561 / 2.85 ( 1451) metal coordination : bond 0.01021 / 0.39 ( 4) metal coordination : angle 2.18906 / 1.17 ( 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 110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 259 ASP cc_start: 0.7674 (t70) cc_final: 0.7347 (t0) REVERT: A 353 GLN cc_start: 0.6001 (tm-30) cc_final: 0.5383 (tm-30) REVERT: A 357 GLN cc_start: 0.6663 (tp40) cc_final: 0.6391 (tp40) REVERT: A 375 ARG cc_start: 0.7381 (tpp80) cc_final: 0.6622 (mtt-85) REVERT: A 379 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.6890 (mtm110) REVERT: A 526 LYS cc_start: 0.5722 (mttp) cc_final: 0.5226 (mtpt) REVERT: A 649 GLU cc_start: 0.8151 (mp0) cc_final: 0.7669 (tt0) REVERT: A 654 LYS cc_start: 0.7828 (mttt) cc_final: 0.7386 (mmtp) REVERT: A 686 LYS cc_start: 0.7969 (tttt) cc_final: 0.7489 (ttmt) REVERT: A 737 LYS cc_start: 0.7860 (mttt) cc_final: 0.7390 (mmtm) REVERT: A 748 GLN cc_start: 0.7732 (mp10) cc_final: 0.7350 (mp10) REVERT: A 839 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 908 MET cc_start: 0.8296 (mpp) cc_final: 0.7283 (mpp) REVERT: A 1017 LYS cc_start: 0.6656 (tttt) cc_final: 0.5924 (tmtt) REVERT: A 1026 THR cc_start: 0.7418 (m) cc_final: 0.7157 (p) REVERT: A 1051 SER cc_start: 0.7886 (t) cc_final: 0.7665 (p) REVERT: A 1166 LEU cc_start: 0.8022 (mt) cc_final: 0.7786 (mp) REVERT: A 1189 TYR cc_start: 0.6036 (p90) cc_final: 0.4302 (m-80) REVERT: A 1229 MET cc_start: 0.7579 (mmp) cc_final: 0.5067 (ttp) REVERT: A 1248 MET cc_start: 0.7484 (tpt) cc_final: 0.6925 (tpt) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1186 time to fit residues: 16.7897 Evaluate side-chains 95 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 58 optimal weight: 0.0470 chunk 13 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.0670 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 640 ASN A1059 GLN A1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.195109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144185 restraints weight = 9545.859| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.85 r_work: 0.3413 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9942 Z= 0.107 Angle : 0.474 7.131 13625 Z= 0.259 Chirality : 0.039 0.203 1518 Planarity : 0.004 0.045 1513 Dihedral : 17.654 149.888 1800 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.17 % Allowed : 9.76 % Favored : 89.08 % 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 are not related in a simple way. whole: 2.08 (0.27), residues: 1026 helix: 2.10 (0.21), residues: 619 sheet: -0.81 (0.68), residues: 47 loop : 0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.010 0.001 TYR A1112 PHE 0.022 0.001 PHE A 994 TRP 0.010 0.001 TRP A1224 HIS 0.002 0.000 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9938) covalent geometry : angle 0.47322 / 0.26 (13622) hydrogen bonds : bond 0.03414 / 2.25 ( 505) hydrogen bonds : angle 3.98750 / 2.76 ( 1451) metal coordination : bond 0.00873 / 0.33 ( 4) metal coordination : angle 1.98915 / 1.06 ( 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: 11 poor density : 90 time to evaluate : 0.259 Fit side-chains REVERT: A 259 ASP cc_start: 0.7640 (t70) cc_final: 0.7299 (t0) REVERT: A 266 MET cc_start: 0.7588 (tpp) cc_final: 0.7115 (tpt) REVERT: A 353 GLN cc_start: 0.5983 (tm-30) cc_final: 0.5362 (tm-30) REVERT: A 357 GLN cc_start: 0.6577 (tp40) cc_final: 0.6284 (tp40) REVERT: A 375 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6480 (mtt-85) REVERT: A 379 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.6764 (mtm110) REVERT: A 636 LYS cc_start: 0.7212 (mtmm) cc_final: 0.6771 (ptpp) REVERT: A 649 GLU cc_start: 0.8123 (mp0) cc_final: 0.7585 (tt0) REVERT: A 654 LYS cc_start: 0.7726 (mttt) cc_final: 0.7265 (mmtp) REVERT: A 686 LYS cc_start: 0.7838 (tttt) cc_final: 0.7368 (ttmt) REVERT: A 737 LYS cc_start: 0.7782 (mttt) cc_final: 0.7299 (mmtm) REVERT: A 748 GLN cc_start: 0.7730 (mp10) cc_final: 0.7335 (mp10) REVERT: A 772 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7753 (mm-40) REVERT: A 1017 LYS cc_start: 0.6582 (tttt) cc_final: 0.5887 (tmtt) REVERT: A 1026 THR cc_start: 0.7289 (m) cc_final: 0.7032 (p) REVERT: A 1121 ILE cc_start: 0.7226 (tt) cc_final: 0.6946 (pt) REVERT: A 1229 MET cc_start: 0.7413 (mmp) cc_final: 0.4885 (ttp) REVERT: A 1248 MET cc_start: 0.7357 (tpt) cc_final: 0.6837 (tpt) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 0.0958 time to fit residues: 12.8646 Evaluate side-chains 91 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.190144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138690 restraints weight = 9572.408| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.84 r_work: 0.3400 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9942 Z= 0.172 Angle : 0.524 7.168 13625 Z= 0.279 Chirality : 0.041 0.181 1518 Planarity : 0.004 0.044 1513 Dihedral : 17.674 148.496 1800 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.80 % Allowed : 9.86 % Favored : 88.34 % 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: 1.87 (0.27), residues: 1026 helix: 1.93 (0.21), residues: 619 sheet: -0.98 (0.69), residues: 47 loop : 0.48 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1052 TYR 0.015 0.002 TYR A1112 PHE 0.020 0.002 PHE A 994 TRP 0.008 0.001 TRP A1219 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 9938) covalent geometry : angle 0.52300 / 0.28 (13622) hydrogen bonds : bond 0.03663 / 2.43 ( 505) hydrogen bonds : angle 4.08239 / 2.84 ( 1451) metal coordination : bond 0.01048 / 0.41 ( 4) metal coordination : angle 2.26393 / 1.18 ( 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 114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.314 Fit side-chains REVERT: A 259 ASP cc_start: 0.7670 (t70) cc_final: 0.7329 (t0) REVERT: A 353 GLN cc_start: 0.6017 (tm-30) cc_final: 0.5338 (tm-30) REVERT: A 357 GLN cc_start: 0.6672 (tp40) cc_final: 0.6338 (tp40) REVERT: A 375 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6567 (mtt-85) REVERT: A 379 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.6867 (mtm110) REVERT: A 526 LYS cc_start: 0.5873 (mttp) cc_final: 0.5271 (mtpt) REVERT: A 636 LYS cc_start: 0.7361 (mtmm) cc_final: 0.7059 (ptpp) REVERT: A 649 GLU cc_start: 0.8177 (mp0) cc_final: 0.7583 (tt0) REVERT: A 654 LYS cc_start: 0.7837 (mttt) cc_final: 0.7375 (mmtt) REVERT: A 686 LYS cc_start: 0.7963 (tttt) cc_final: 0.7376 (ttmt) REVERT: A 737 LYS cc_start: 0.7900 (mttt) cc_final: 0.7413 (mmtm) REVERT: A 748 GLN cc_start: 0.7866 (mp10) cc_final: 0.7502 (mp10) REVERT: A 772 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 835 THR cc_start: 0.7862 (m) cc_final: 0.7587 (p) REVERT: A 945 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6487 (mtt-85) REVERT: A 994 PHE cc_start: 0.7514 (t80) cc_final: 0.7194 (t80) REVERT: A 1017 LYS cc_start: 0.6761 (tttt) cc_final: 0.5875 (tmtt) REVERT: A 1026 THR cc_start: 0.7429 (m) cc_final: 0.7141 (p) REVERT: A 1121 ILE cc_start: 0.7399 (tt) cc_final: 0.7077 (pt) REVERT: A 1189 TYR cc_start: 0.6041 (p90) cc_final: 0.4337 (m-80) REVERT: A 1229 MET cc_start: 0.7626 (mmp) cc_final: 0.5035 (ttp) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.1188 time to fit residues: 17.6916 Evaluate side-chains 105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 0.0040 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** 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 = 0.4110 r_free = 0.4110 target = 0.191431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143822 restraints weight = 9365.564| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.60 r_work: 0.3363 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9942 Z= 0.126 Angle : 0.493 8.600 13625 Z= 0.264 Chirality : 0.040 0.183 1518 Planarity : 0.004 0.042 1513 Dihedral : 17.659 146.722 1800 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.38 % Allowed : 10.92 % Favored : 87.70 % 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: 1.90 (0.27), residues: 1026 helix: 1.99 (0.21), residues: 619 sheet: -1.02 (0.69), residues: 47 loop : 0.41 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1129 TYR 0.012 0.001 TYR A1112 PHE 0.011 0.001 PHE A 994 TRP 0.009 0.001 TRP A1036 HIS 0.002 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9938) covalent geometry : angle 0.49231 / 0.26 (13622) hydrogen bonds : bond 0.03471 / 2.30 ( 505) hydrogen bonds : angle 4.01325 / 2.79 ( 1451) metal coordination : bond 0.01077 / 0.41 ( 4) metal coordination : angle 2.09311 / 1.13 ( 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 110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.200 Fit side-chains REVERT: A 259 ASP cc_start: 0.7687 (t70) cc_final: 0.7346 (t0) REVERT: A 353 GLN cc_start: 0.6090 (tm-30) cc_final: 0.5580 (tm-30) REVERT: A 357 GLN cc_start: 0.6738 (tp40) cc_final: 0.6401 (tp40) REVERT: A 375 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6573 (mtt-85) REVERT: A 379 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6835 (mtm110) REVERT: A 636 LYS cc_start: 0.7339 (mtmm) cc_final: 0.7033 (ptpp) REVERT: A 649 GLU cc_start: 0.8136 (mp0) cc_final: 0.7540 (tt0) REVERT: A 654 LYS cc_start: 0.7853 (mttt) cc_final: 0.7427 (mmtp) REVERT: A 686 LYS cc_start: 0.7967 (tttt) cc_final: 0.7336 (ttmt) REVERT: A 737 LYS cc_start: 0.7939 (mttt) cc_final: 0.7457 (mmtm) REVERT: A 748 GLN cc_start: 0.7843 (mp10) cc_final: 0.7477 (mp10) REVERT: A 772 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8114 (mm-40) REVERT: A 835 THR cc_start: 0.7889 (m) cc_final: 0.7583 (p) REVERT: A 945 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6516 (mtt-85) REVERT: A 1017 LYS cc_start: 0.6757 (tttt) cc_final: 0.6467 (tptt) REVERT: A 1026 THR cc_start: 0.7446 (m) cc_final: 0.7160 (p) REVERT: A 1121 ILE cc_start: 0.7381 (tt) cc_final: 0.7051 (pt) REVERT: A 1189 TYR cc_start: 0.6078 (p90) cc_final: 0.4361 (m-80) REVERT: A 1229 MET cc_start: 0.7663 (mmp) cc_final: 0.5070 (ttp) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.0976 time to fit residues: 13.8443 Evaluate side-chains 102 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 LYS 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 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: 0.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4181 r_free = 0.4181 target = 0.194093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141837 restraints weight = 9801.538| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.93 r_work: 0.3443 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9942 Z= 0.167 Angle : 0.521 6.743 13625 Z= 0.279 Chirality : 0.041 0.187 1518 Planarity : 0.004 0.042 1513 Dihedral : 17.682 146.254 1800 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 10.50 % Favored : 87.70 % 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: 1.75 (0.27), residues: 1026 helix: 1.86 (0.21), residues: 619 sheet: -1.16 (0.71), residues: 47 loop : 0.38 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1052 TYR 0.014 0.002 TYR A1112 PHE 0.021 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 0.00398 / 0.17 ( 9938) covalent geometry : angle 0.52011 / 0.28 (13622) hydrogen bonds : bond 0.03634 / 2.41 ( 505) hydrogen bonds : angle 4.08031 / 2.85 ( 1451) metal coordination : bond 0.01081 / 0.42 ( 4) metal coordination : angle 2.43790 / 1.29 ( 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 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.258 Fit side-chains REVERT: A 259 ASP cc_start: 0.7889 (t70) cc_final: 0.7616 (t0) REVERT: A 266 MET cc_start: 0.7996 (tpp) cc_final: 0.7666 (mmm) REVERT: A 353 GLN cc_start: 0.6241 (tm-30) cc_final: 0.5702 (tm-30) REVERT: A 357 GLN cc_start: 0.7055 (tp40) cc_final: 0.6710 (tp40) REVERT: A 375 ARG cc_start: 0.7560 (tpp80) cc_final: 0.6805 (mtt-85) REVERT: A 379 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7002 (mtm110) REVERT: A 526 LYS cc_start: 0.6123 (mttp) cc_final: 0.5582 (mtpt) REVERT: A 649 GLU cc_start: 0.8180 (mp0) cc_final: 0.7792 (tt0) REVERT: A 654 LYS cc_start: 0.8037 (mttt) cc_final: 0.7715 (mmtt) REVERT: A 686 LYS cc_start: 0.8262 (tttt) cc_final: 0.7715 (ttmt) REVERT: A 737 LYS cc_start: 0.8126 (mttt) cc_final: 0.7704 (mmtm) REVERT: A 748 GLN cc_start: 0.7772 (mp10) cc_final: 0.7513 (mp10) REVERT: A 772 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7971 (mm-40) REVERT: A 835 THR cc_start: 0.8196 (m) cc_final: 0.7888 (p) REVERT: A 945 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.6775 (mtt-85) REVERT: A 1017 LYS cc_start: 0.7035 (tttt) cc_final: 0.6761 (tptt) REVERT: A 1026 THR cc_start: 0.7835 (m) cc_final: 0.7609 (p) REVERT: A 1189 TYR cc_start: 0.6576 (p90) cc_final: 0.4944 (m-80) REVERT: A 1229 MET cc_start: 0.7914 (mmp) cc_final: 0.5494 (ttt) REVERT: A 1248 MET cc_start: 0.7617 (tpt) cc_final: 0.7226 (tpt) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.0966 time to fit residues: 14.5852 Evaluate side-chains 107 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 640 ASN 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.724 > 50: distance: 90 - 107: 29.216 distance: 94 - 115: 26.869 distance: 99 - 123: 20.865 distance: 102 - 107: 28.414 distance: 103 - 132: 28.951 distance: 107 - 108: 21.212 distance: 108 - 109: 25.627 distance: 108 - 111: 12.962 distance: 109 - 110: 33.084 distance: 109 - 115: 14.692 distance: 111 - 112: 28.766 distance: 112 - 113: 16.435 distance: 112 - 114: 10.837 distance: 115 - 116: 8.616 distance: 116 - 117: 10.114 distance: 116 - 119: 8.500 distance: 117 - 118: 15.563 distance: 117 - 123: 15.189 distance: 120 - 121: 37.093 distance: 120 - 122: 29.390 distance: 123 - 124: 4.011 distance: 124 - 125: 18.356 distance: 124 - 127: 28.492 distance: 125 - 132: 5.493 distance: 127 - 128: 22.450 distance: 128 - 129: 24.499 distance: 129 - 130: 39.967 distance: 130 - 131: 24.724 distance: 132 - 133: 31.675 distance: 133 - 134: 15.382 distance: 133 - 136: 41.740 distance: 134 - 135: 22.536 distance: 134 - 140: 24.350 distance: 136 - 137: 46.010 distance: 137 - 138: 6.263 distance: 140 - 141: 31.010 distance: 141 - 142: 36.986 distance: 142 - 143: 25.415 distance: 142 - 144: 47.135 distance: 144 - 145: 45.734 distance: 145 - 146: 11.075 distance: 145 - 148: 32.425 distance: 146 - 147: 34.868 distance: 146 - 152: 15.617 distance: 148 - 149: 34.864 distance: 148 - 150: 10.697 distance: 149 - 151: 12.850 distance: 152 - 153: 28.559 distance: 153 - 154: 18.778 distance: 153 - 156: 10.736 distance: 154 - 155: 16.508 distance: 154 - 160: 12.968 distance: 156 - 157: 9.590 distance: 157 - 158: 14.703 distance: 157 - 159: 35.441 distance: 160 - 161: 16.531 distance: 161 - 162: 18.614 distance: 163 - 194: 31.600 distance: 164 - 165: 22.824 distance: 165 - 166: 18.142 distance: 165 - 168: 14.608 distance: 166 - 167: 34.268 distance: 166 - 171: 10.848 distance: 167 - 202: 29.639 distance: 168 - 169: 6.330 distance: 168 - 170: 8.362 distance: 172 - 173: 40.166 distance: 172 - 175: 21.759 distance: 173 - 174: 12.192 distance: 173 - 183: 19.893 distance: 174 - 210: 25.660 distance: 175 - 176: 16.144 distance: 176 - 177: 17.418 distance: 176 - 178: 16.230 distance: 177 - 179: 27.652 distance: 178 - 180: 13.807 distance: 179 - 181: 19.848 distance: 180 - 181: 15.391 distance: 181 - 182: 16.998