Starting phenix.real_space_refine on Wed Mar 4 05:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.map" model { file = "/net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1x_23626/03_2026/7m1x_23626.cif" } resolution = 3.7 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 12 5.16 5 C 6350 2.51 5 N 2156 2.21 5 O 2685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11475 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2806 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2770 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 715 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 2.42, per 1000 atoms: 0.21 Number of scatterers: 11475 At special positions: 0 Unit cell: (102.3, 121, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 272 15.00 O 2685 8.00 N 2156 7.00 C 6350 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: 0.84 Conformation dependent library (CDL) restraints added in 391.4 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 74.3% alpha, 1.9% beta 135 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.607A pdb=" N PHE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 514 removed outlier: 3.627A pdb=" N ALA A 514 " --> pdb=" O CYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.780A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.842A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.526A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 824 Processing helix chain 'C' and resid 828 through 838 Processing helix chain 'C' and resid 847 through 875 removed outlier: 4.054A pdb=" N ALA C 851 " --> pdb=" O GLY C 847 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 875 " --> pdb=" O ASN C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 893 removed outlier: 3.529A pdb=" N ASP C 893 " --> pdb=" O ALA C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 900 Processing helix chain 'D' and resid 1234 through 1246 Processing helix chain 'D' and resid 1252 through 1281 Processing helix chain 'D' and resid 1287 through 1299 removed outlier: 3.697A pdb=" N ILE D1291 " --> pdb=" O THR D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1300 through 1320 Processing helix chain 'E' and resid 644 through 657 Processing helix chain 'E' and resid 663 through 679 removed outlier: 4.259A pdb=" N ASP E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE E 678 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 714 Processing helix chain 'E' and resid 720 through 732 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.707A pdb=" N ILE F 229 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 249 through 276 removed outlier: 4.193A pdb=" N GLU F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.512A pdb=" N VAL F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 1018 through 1023 Processing helix chain 'G' and resid 1028 through 1039 removed outlier: 3.709A pdb=" N SER G1038 " --> pdb=" O ARG G1034 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G1039 " --> pdb=" O HIS G1035 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1077 removed outlier: 3.796A pdb=" N VAL G1052 " --> pdb=" O ALA G1048 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G1053 " --> pdb=" O THR G1049 " (cutoff:3.500A) Processing helix chain 'G' and resid 1082 through 1093 Processing helix chain 'G' and resid 1093 through 1100 removed outlier: 3.737A pdb=" N ASP G1097 " --> pdb=" O ASP G1093 " (cutoff:3.500A) Processing helix chain 'H' and resid 1434 through 1446 Processing helix chain 'H' and resid 1452 through 1481 Processing helix chain 'H' and resid 1487 through 1499 removed outlier: 3.698A pdb=" N ILE H1491 " --> pdb=" O THR H1487 " (cutoff:3.500A) Processing helix chain 'H' and resid 1500 through 1520 Processing sheet with id=AA1, first strand: chain 'A' and resid 483 through 484 removed outlier: 6.999A pdb=" N ARG A 483 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 845 through 846 removed outlier: 7.216A pdb=" N ARG C 845 " --> pdb=" O ILE D1286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 880 through 881 Processing sheet with id=AA4, first strand: chain 'E' and resid 683 through 684 removed outlier: 7.173A pdb=" N ARG E 683 " --> pdb=" O VAL F 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 718 through 719 Processing sheet with id=AA6, first strand: chain 'G' and resid 1045 through 1046 removed outlier: 7.156A pdb=" N ARG G1045 " --> pdb=" O ILE H1486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 1080 through 1081 399 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1924 1.33 - 1.45: 4086 1.45 - 1.56: 5656 1.56 - 1.68: 542 1.68 - 1.80: 22 Bond restraints: 12230 Sorted by residual: bond pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" C3' DT I 15 " pdb=" O3' DT I 15 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB THR F 254 " pdb=" CG2 THR F 254 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB VAL H1463 " pdb=" CG2 VAL H1463 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 ... (remaining 12225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 16621 1.55 - 3.09: 939 3.09 - 4.64: 96 4.64 - 6.19: 15 6.19 - 7.73: 7 Bond angle restraints: 17678 Sorted by residual: angle pdb=" N VAL A 517 " pdb=" CA VAL A 517 " pdb=" C VAL A 517 " ideal model delta sigma weight residual 113.20 107.72 5.48 9.60e-01 1.09e+00 3.25e+01 angle pdb=" N GLY D1301 " pdb=" CA GLY D1301 " pdb=" C GLY D1301 " ideal model delta sigma weight residual 113.18 120.91 -7.73 2.37e+00 1.78e-01 1.06e+01 angle pdb=" N GLY H1501 " pdb=" CA GLY H1501 " pdb=" C GLY H1501 " ideal model delta sigma weight residual 113.18 120.88 -7.70 2.37e+00 1.78e-01 1.06e+01 angle pdb=" N SER C 842 " pdb=" CA SER C 842 " pdb=" C SER C 842 " ideal model delta sigma weight residual 110.80 117.56 -6.76 2.13e+00 2.20e-01 1.01e+01 angle pdb=" C THR C 841 " pdb=" N SER C 842 " pdb=" CA SER C 842 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5212 35.46 - 70.92: 1413 70.92 - 106.37: 16 106.37 - 141.83: 2 141.83 - 177.29: 3 Dihedral angle restraints: 6646 sinusoidal: 4484 harmonic: 2162 Sorted by residual: dihedral pdb=" CA THR C 841 " pdb=" C THR C 841 " pdb=" N SER C 842 " pdb=" CA SER C 842 " ideal model delta harmonic sigma weight residual -180.00 -142.85 -37.15 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA PRO H1500 " pdb=" C PRO H1500 " pdb=" N GLY H1501 " pdb=" CA GLY H1501 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PRO D1300 " pdb=" C PRO D1300 " pdb=" N GLY D1301 " pdb=" CA GLY D1301 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1234 0.034 - 0.068: 560 0.068 - 0.101: 168 0.101 - 0.135: 46 0.135 - 0.169: 11 Chirality restraints: 2019 Sorted by residual: chirality pdb=" P DA I -31 " pdb=" OP1 DA I -31 " pdb=" OP2 DA I -31 " pdb=" O5' DA I -31 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 2016 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 882 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO C 883 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 883 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 883 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 14 " 0.028 2.00e-02 2.50e+03 1.36e-02 4.63e+00 pdb=" N1 DT I 14 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT I 14 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 14 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 14 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 14 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 14 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 14 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 14 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 14 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G1082 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO G1083 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO G1083 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G1083 " -0.030 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2360 2.78 - 3.31: 10154 3.31 - 3.84: 23712 3.84 - 4.37: 25913 4.37 - 4.90: 36424 Nonbonded interactions: 98563 Sorted by model distance: nonbonded pdb=" OG SER G1073 " pdb=" O VAL G1078 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 842 " pdb=" O THR G1041 " model vdw 2.254 3.040 nonbonded pdb=" O ILE E 719 " pdb=" OG SER F 247 " model vdw 2.265 3.040 nonbonded pdb=" O GLY C 906 " pdb=" OG1 THR E 658 " model vdw 2.288 3.040 nonbonded pdb=" O SER C 916 " pdb=" OG SER C 916 " model vdw 2.298 3.040 ... (remaining 98558 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 641 through 735) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 223 through 302) } ncs_group { reference = (chain 'C' and resid 816 through 910) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue 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: 0.730 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.020 Find NCS groups from input model: 0.110 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 0.055 12230 Z= 0.316 Angle : 0.779 7.733 17678 Z= 0.467 Chirality : 0.042 0.169 2019 Planarity : 0.005 0.065 1290 Dihedral : 29.133 177.288 5250 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 2.27 % Allowed : 6.63 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.56 (0.27), residues: 730 helix: -0.21 (0.20), residues: 526 sheet: None (None), residues: 0 loop : -3.11 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1031 TYR 0.015 0.002 TYR C 860 PHE 0.018 0.002 PHE A 478 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00698 (12230) covalent geometry : angle 0.77919 (17678) hydrogen bonds : bond 0.09819 ( 746) hydrogen bonds : angle 4.08767 ( 1879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 346 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9232 (tt0) cc_final: 0.8532 (tm-30) REVERT: A 473 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 476 GLN cc_start: 0.9020 (tp40) cc_final: 0.8672 (tm-30) REVERT: A 493 GLN cc_start: 0.8856 (tt0) cc_final: 0.8593 (tt0) REVERT: A 520 MET cc_start: 0.8227 (mtt) cc_final: 0.7452 (mtp) REVERT: A 522 LYS cc_start: 0.8580 (pttt) cc_final: 0.8332 (ptpp) REVERT: A 534 ARG cc_start: 0.8265 (ptp90) cc_final: 0.7827 (ttp80) REVERT: B 29 ILE cc_start: 0.9491 (mm) cc_final: 0.9288 (mm) REVERT: B 46 ILE cc_start: 0.8745 (mt) cc_final: 0.8534 (mt) REVERT: B 52 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8685 (tp30) REVERT: B 74 GLU cc_start: 0.9313 (tt0) cc_final: 0.9085 (tt0) REVERT: B 88 TYR cc_start: 0.8668 (m-10) cc_final: 0.8382 (m-80) REVERT: B 92 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8522 (mtp-110) REVERT: B 98 TYR cc_start: 0.9137 (m-10) cc_final: 0.8871 (m-80) REVERT: C 821 GLN cc_start: 0.9179 (mp10) cc_final: 0.8943 (mp10) REVERT: C 839 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8278 (mtm-85) REVERT: C 853 TYR cc_start: 0.8956 (t80) cc_final: 0.8400 (t80) REVERT: C 887 GLN cc_start: 0.9200 (tp40) cc_final: 0.8865 (tp-100) REVERT: C 901 LYS cc_start: 0.9030 (pttp) cc_final: 0.8403 (tptp) REVERT: C 912 HIS cc_start: 0.8481 (t70) cc_final: 0.7714 (t-90) REVERT: D 1248 ASP cc_start: 0.8506 (p0) cc_final: 0.8279 (p0) REVERT: D 1265 ASP cc_start: 0.8648 (t70) cc_final: 0.8419 (t0) REVERT: D 1268 GLU cc_start: 0.8987 (tp30) cc_final: 0.8664 (tp30) REVERT: D 1277 LEU cc_start: 0.9197 (tp) cc_final: 0.8990 (tp) REVERT: D 1279 HIS cc_start: 0.8670 (t-90) cc_final: 0.8224 (t70) REVERT: D 1281 ASN cc_start: 0.9413 (t0) cc_final: 0.8995 (t0) REVERT: D 1303 LEU cc_start: 0.9047 (tp) cc_final: 0.8843 (tp) REVERT: D 1317 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8957 (ttmt) REVERT: E 659 GLU cc_start: 0.8390 (pp20) cc_final: 0.8095 (pp20) REVERT: E 660 LEU cc_start: 0.8873 (mm) cc_final: 0.8495 (mm) REVERT: E 661 LEU cc_start: 0.8987 (mt) cc_final: 0.8705 (mt) REVERT: E 668 GLN cc_start: 0.9271 (tt0) cc_final: 0.7953 (tm-30) REVERT: E 690 MET cc_start: 0.9194 (tpt) cc_final: 0.8972 (tpp) REVERT: E 693 GLN cc_start: 0.9034 (tt0) cc_final: 0.8761 (tp40) REVERT: E 706 ASP cc_start: 0.9207 (t70) cc_final: 0.8986 (t70) REVERT: E 718 THR cc_start: 0.8792 (p) cc_final: 0.7902 (p) REVERT: E 722 LYS cc_start: 0.8969 (pttt) cc_final: 0.8706 (pttm) REVERT: E 723 ASP cc_start: 0.8840 (m-30) cc_final: 0.8613 (m-30) REVERT: E 725 GLN cc_start: 0.9256 (mt0) cc_final: 0.8959 (mt0) REVERT: F 231 LYS cc_start: 0.8817 (tttt) cc_final: 0.8487 (ttpt) REVERT: F 243 VAL cc_start: 0.9290 (t) cc_final: 0.9033 (p) REVERT: F 244 LYS cc_start: 0.8900 (tttt) cc_final: 0.8292 (tttt) REVERT: F 246 ILE cc_start: 0.9137 (mt) cc_final: 0.8817 (pt) REVERT: F 249 LEU cc_start: 0.9427 (mt) cc_final: 0.9036 (mm) REVERT: F 258 LEU cc_start: 0.9632 (tp) cc_final: 0.9404 (tp) REVERT: F 274 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8933 (tm-30) REVERT: F 291 LYS cc_start: 0.9158 (tttp) cc_final: 0.8816 (ttpt) REVERT: G 1059 GLU cc_start: 0.8798 (tt0) cc_final: 0.8557 (tt0) REVERT: G 1084 ARG cc_start: 0.8739 (tpt170) cc_final: 0.8512 (tpp80) REVERT: G 1087 GLN cc_start: 0.9156 (tp40) cc_final: 0.8929 (tp40) REVERT: G 1088 LEU cc_start: 0.9347 (mm) cc_final: 0.8950 (mm) REVERT: G 1093 ASP cc_start: 0.8276 (t70) cc_final: 0.8010 (t0) REVERT: H 1433 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8616 (m) REVERT: H 1461 SER cc_start: 0.9526 (t) cc_final: 0.9325 (t) REVERT: H 1465 ASP cc_start: 0.9202 (t70) cc_final: 0.8849 (t0) REVERT: H 1468 GLU cc_start: 0.8762 (tp30) cc_final: 0.8351 (tt0) REVERT: H 1486 ILE cc_start: 0.8916 (mt) cc_final: 0.8685 (mt) REVERT: H 1505 LYS cc_start: 0.9207 (tmmt) cc_final: 0.8997 (mttm) outliers start: 14 outliers final: 5 residues processed: 354 average time/residue: 0.1241 time to fit residues: 58.3822 Evaluate side-chains 287 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1453 SER Chi-restraints excluded: chain H residue 1488 SER Chi-restraints excluded: chain H residue 1495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 476 GLN B 25 ASN B 75 HIS D1246 HIS E 655 GLN E 668 GLN E 693 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1087 GLN H1446 HIS H1481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.098170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070875 restraints weight = 32110.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073083 restraints weight = 15244.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074572 restraints weight = 10125.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075467 restraints weight = 8056.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075937 restraints weight = 7107.919| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12230 Z= 0.172 Angle : 0.618 7.022 17678 Z= 0.362 Chirality : 0.035 0.146 2019 Planarity : 0.004 0.055 1290 Dihedral : 31.511 174.737 3809 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.53 % Allowed : 23.95 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.37 (0.30), residues: 730 helix: 1.34 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.93 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.019 0.001 TYR D1318 PHE 0.007 0.001 PHE E 667 HIS 0.006 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00375 (12230) covalent geometry : angle 0.61763 (17678) hydrogen bonds : bond 0.03810 ( 746) hydrogen bonds : angle 3.15821 ( 1879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9042 (tt0) cc_final: 0.8492 (tm-30) REVERT: A 473 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 485 GLN cc_start: 0.8829 (mt0) cc_final: 0.8336 (mt0) REVERT: A 520 MET cc_start: 0.8150 (mtt) cc_final: 0.7604 (mtp) REVERT: B 52 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8449 (tp30) REVERT: B 81 VAL cc_start: 0.9376 (t) cc_final: 0.9017 (p) REVERT: B 92 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8004 (tmm-80) REVERT: C 822 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8875 (ttt-90) REVERT: C 826 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7637 (mm110) REVERT: C 853 TYR cc_start: 0.8794 (t80) cc_final: 0.8151 (t80) REVERT: C 867 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 884 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8604 (tpt170) REVERT: C 887 GLN cc_start: 0.9200 (tp40) cc_final: 0.8867 (tp-100) REVERT: C 901 LYS cc_start: 0.8945 (pttp) cc_final: 0.8294 (tptp) REVERT: C 912 HIS cc_start: 0.8280 (t70) cc_final: 0.7722 (t-90) REVERT: D 1279 HIS cc_start: 0.8644 (t-90) cc_final: 0.8091 (t70) REVERT: D 1281 ASN cc_start: 0.9339 (t0) cc_final: 0.8903 (t0) REVERT: D 1317 LYS cc_start: 0.9323 (ttmm) cc_final: 0.8978 (ttmt) REVERT: E 656 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8826 (ptpp) REVERT: E 705 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8515 (tm-30) REVERT: E 720 MET cc_start: 0.8708 (tpp) cc_final: 0.8270 (mmm) REVERT: E 722 LYS cc_start: 0.8881 (pttt) cc_final: 0.8611 (ptpp) REVERT: E 725 GLN cc_start: 0.9205 (mt0) cc_final: 0.8920 (mt0) REVERT: E 733 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7719 (pt0) REVERT: F 231 LYS cc_start: 0.8853 (tttt) cc_final: 0.8554 (ttpt) REVERT: F 243 VAL cc_start: 0.9423 (t) cc_final: 0.9222 (p) REVERT: F 244 LYS cc_start: 0.9077 (tttt) cc_final: 0.8800 (tttt) REVERT: F 274 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8746 (tm-30) REVERT: F 284 MET cc_start: 0.8942 (tpp) cc_final: 0.8415 (mmm) REVERT: F 291 LYS cc_start: 0.9073 (tttp) cc_final: 0.8725 (ttpt) REVERT: G 1045 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8881 (ptm160) REVERT: G 1059 GLU cc_start: 0.8664 (tt0) cc_final: 0.8463 (tt0) REVERT: G 1084 ARG cc_start: 0.8928 (tpt170) cc_final: 0.8612 (tpp80) REVERT: G 1087 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8852 (tp40) REVERT: G 1088 LEU cc_start: 0.9303 (mm) cc_final: 0.8987 (mm) REVERT: H 1433 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8809 (m) REVERT: H 1461 SER cc_start: 0.9482 (t) cc_final: 0.9259 (t) REVERT: H 1465 ASP cc_start: 0.9247 (t70) cc_final: 0.9047 (t0) REVERT: H 1468 GLU cc_start: 0.8589 (tp30) cc_final: 0.8303 (tt0) REVERT: H 1486 ILE cc_start: 0.9004 (mt) cc_final: 0.8584 (mt) REVERT: H 1490 GLU cc_start: 0.8950 (mp0) cc_final: 0.8627 (mp0) outliers start: 28 outliers final: 18 residues processed: 319 average time/residue: 0.1186 time to fit residues: 51.1418 Evaluate side-chains 297 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1045 ARG Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN E 668 GLN G1033 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066590 restraints weight = 32921.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068650 restraints weight = 16668.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070061 restraints weight = 11450.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.070873 restraints weight = 9267.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071320 restraints weight = 8263.871| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12230 Z= 0.273 Angle : 0.659 7.567 17678 Z= 0.385 Chirality : 0.037 0.161 2019 Planarity : 0.004 0.055 1290 Dihedral : 31.393 173.604 3806 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 7.61 % Allowed : 25.73 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.84 (0.30), residues: 730 helix: 1.69 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.89 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 245 TYR 0.025 0.002 TYR D1318 PHE 0.015 0.002 PHE D1267 HIS 0.008 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00606 (12230) covalent geometry : angle 0.65937 (17678) hydrogen bonds : bond 0.04481 ( 746) hydrogen bonds : angle 3.37787 ( 1879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8014 (pp20) cc_final: 0.7722 (pp20) REVERT: A 468 GLN cc_start: 0.9148 (tt0) cc_final: 0.8596 (tm-30) REVERT: A 473 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 493 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (tp40) REVERT: A 520 MET cc_start: 0.8379 (mtt) cc_final: 0.7960 (mtp) REVERT: B 88 TYR cc_start: 0.8570 (m-10) cc_final: 0.8369 (m-10) REVERT: B 92 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8205 (tmm-80) REVERT: C 821 GLN cc_start: 0.9106 (mp10) cc_final: 0.8557 (mp10) REVERT: C 822 ARG cc_start: 0.9147 (ttp80) cc_final: 0.8856 (ttt-90) REVERT: C 853 TYR cc_start: 0.8807 (t80) cc_final: 0.8094 (t80) REVERT: C 867 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 887 GLN cc_start: 0.9213 (tp40) cc_final: 0.8123 (tp-100) REVERT: C 901 LYS cc_start: 0.8876 (pttp) cc_final: 0.8359 (tptp) REVERT: C 912 HIS cc_start: 0.8328 (t70) cc_final: 0.7737 (t-90) REVERT: D 1281 ASN cc_start: 0.9355 (t0) cc_final: 0.8941 (t0) REVERT: D 1317 LYS cc_start: 0.9358 (ttmm) cc_final: 0.9036 (ttmt) REVERT: E 690 MET cc_start: 0.9009 (mmm) cc_final: 0.8701 (tpp) REVERT: E 693 GLN cc_start: 0.9370 (tp40) cc_final: 0.8952 (tp40) REVERT: E 694 GLU cc_start: 0.9036 (tp30) cc_final: 0.8600 (tp30) REVERT: E 697 GLU cc_start: 0.7839 (pp20) cc_final: 0.7423 (pp20) REVERT: E 705 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 722 LYS cc_start: 0.8921 (pttt) cc_final: 0.8683 (ptpp) REVERT: E 725 GLN cc_start: 0.9282 (mt0) cc_final: 0.8970 (mt0) REVERT: F 231 LYS cc_start: 0.9069 (tttt) cc_final: 0.8835 (ttmt) REVERT: F 244 LYS cc_start: 0.9062 (tttt) cc_final: 0.8812 (tttt) REVERT: F 252 GLU cc_start: 0.8764 (mp0) cc_final: 0.8534 (mp0) REVERT: F 274 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 279 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8454 (mtpt) REVERT: F 291 LYS cc_start: 0.9144 (tttp) cc_final: 0.8860 (ttpt) REVERT: G 1059 GLU cc_start: 0.8677 (tt0) cc_final: 0.8448 (tt0) REVERT: G 1077 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9075 (mmmt) REVERT: G 1079 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9035 (ttpt) REVERT: G 1084 ARG cc_start: 0.8949 (tpt170) cc_final: 0.8480 (tpp80) REVERT: G 1087 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8716 (tp-100) REVERT: G 1088 LEU cc_start: 0.9332 (mm) cc_final: 0.9047 (mm) REVERT: H 1486 ILE cc_start: 0.9124 (mt) cc_final: 0.8809 (mt) outliers start: 47 outliers final: 35 residues processed: 301 average time/residue: 0.1162 time to fit residues: 47.6634 Evaluate side-chains 301 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1061 LEU Chi-restraints excluded: chain G residue 1066 LEU Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1485 THR Chi-restraints excluded: chain H residue 1497 LEU Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.0470 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN E 668 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070260 restraints weight = 33601.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.072479 restraints weight = 16270.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073915 restraints weight = 10848.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074809 restraints weight = 8648.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075304 restraints weight = 7621.366| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12230 Z= 0.170 Angle : 0.618 12.837 17678 Z= 0.360 Chirality : 0.035 0.199 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.221 173.941 3803 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.85 % Allowed : 30.26 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.15 (0.31), residues: 730 helix: 1.90 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1296 TYR 0.023 0.002 TYR H1480 PHE 0.014 0.001 PHE B 61 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00374 (12230) covalent geometry : angle 0.61760 (17678) hydrogen bonds : bond 0.03799 ( 746) hydrogen bonds : angle 3.04161 ( 1879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7968 (pp20) cc_final: 0.7257 (pp20) REVERT: A 468 GLN cc_start: 0.9064 (tt0) cc_final: 0.8461 (tm-30) REVERT: A 473 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 485 GLN cc_start: 0.8717 (mt0) cc_final: 0.8450 (mt0) REVERT: A 520 MET cc_start: 0.8241 (mtt) cc_final: 0.7723 (mtp) REVERT: B 52 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8486 (tp30) REVERT: B 92 ARG cc_start: 0.8867 (tmm-80) cc_final: 0.8093 (tmm-80) REVERT: C 821 GLN cc_start: 0.9065 (mp10) cc_final: 0.8806 (mp10) REVERT: C 822 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8873 (ttt-90) REVERT: C 853 TYR cc_start: 0.8727 (t80) cc_final: 0.8004 (t80) REVERT: C 867 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8774 (tm-30) REVERT: C 875 ASP cc_start: 0.8847 (m-30) cc_final: 0.8332 (p0) REVERT: C 887 GLN cc_start: 0.9151 (tp40) cc_final: 0.8854 (tp-100) REVERT: C 901 LYS cc_start: 0.8771 (pttp) cc_final: 0.8277 (tptp) REVERT: C 912 HIS cc_start: 0.8290 (t70) cc_final: 0.7800 (t-90) REVERT: D 1232 GLU cc_start: 0.7956 (tp30) cc_final: 0.7716 (tp30) REVERT: D 1279 HIS cc_start: 0.8668 (t-90) cc_final: 0.8181 (t70) REVERT: D 1281 ASN cc_start: 0.9300 (t0) cc_final: 0.8899 (t0) REVERT: D 1317 LYS cc_start: 0.9314 (ttmm) cc_final: 0.8975 (ttmt) REVERT: E 668 GLN cc_start: 0.9068 (tt0) cc_final: 0.8105 (tm-30) REVERT: E 690 MET cc_start: 0.8951 (mmm) cc_final: 0.8663 (tpp) REVERT: E 693 GLN cc_start: 0.9343 (tp40) cc_final: 0.8869 (tp40) REVERT: E 705 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8489 (tm-30) REVERT: E 708 ASN cc_start: 0.9357 (t0) cc_final: 0.8990 (t0) REVERT: E 733 GLU cc_start: 0.7914 (pt0) cc_final: 0.7680 (pt0) REVERT: F 231 LYS cc_start: 0.9003 (tttt) cc_final: 0.8797 (ttmt) REVERT: F 274 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 279 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8437 (mtpt) REVERT: G 1045 ARG cc_start: 0.9252 (ptm160) cc_final: 0.8920 (ptm-80) REVERT: G 1059 GLU cc_start: 0.8629 (tt0) cc_final: 0.8391 (tt0) REVERT: G 1077 LYS cc_start: 0.9366 (mmmt) cc_final: 0.9087 (mmmt) REVERT: G 1079 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9039 (ttpt) REVERT: G 1084 ARG cc_start: 0.8953 (tpt170) cc_final: 0.8456 (tpp80) REVERT: G 1087 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8831 (tp40) REVERT: G 1088 LEU cc_start: 0.9312 (mm) cc_final: 0.8982 (mm) REVERT: H 1482 LYS cc_start: 0.9239 (mttt) cc_final: 0.8861 (mmtt) REVERT: H 1486 ILE cc_start: 0.8938 (mt) cc_final: 0.8651 (mt) REVERT: H 1490 GLU cc_start: 0.9099 (mp0) cc_final: 0.8868 (mp0) outliers start: 30 outliers final: 21 residues processed: 307 average time/residue: 0.1182 time to fit residues: 49.2956 Evaluate side-chains 298 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1073 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068531 restraints weight = 33699.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070647 restraints weight = 16711.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072059 restraints weight = 11277.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.072924 restraints weight = 9034.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073419 restraints weight = 7985.165| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12230 Z= 0.231 Angle : 0.627 6.312 17678 Z= 0.370 Chirality : 0.036 0.179 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.237 173.760 3803 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 7.44 % Allowed : 29.94 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.19 (0.31), residues: 730 helix: 1.92 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -2.76 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1296 TYR 0.024 0.002 TYR D1318 PHE 0.014 0.002 PHE D1267 HIS 0.006 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00515 (12230) covalent geometry : angle 0.62731 (17678) hydrogen bonds : bond 0.04222 ( 746) hydrogen bonds : angle 3.20793 ( 1879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7883 (pp20) cc_final: 0.7553 (pp20) REVERT: A 468 GLN cc_start: 0.9149 (tt0) cc_final: 0.8538 (tm-30) REVERT: A 473 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 485 GLN cc_start: 0.8804 (mt0) cc_final: 0.8486 (mt0) REVERT: A 520 MET cc_start: 0.8321 (mtt) cc_final: 0.7911 (mtp) REVERT: B 52 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8565 (tp30) REVERT: B 88 TYR cc_start: 0.8414 (m-10) cc_final: 0.8119 (m-80) REVERT: B 92 ARG cc_start: 0.8880 (tmm-80) cc_final: 0.8395 (tmm-80) REVERT: C 821 GLN cc_start: 0.9090 (mp10) cc_final: 0.8534 (mp10) REVERT: C 822 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8832 (ttt-90) REVERT: C 853 TYR cc_start: 0.8770 (t80) cc_final: 0.8104 (t80) REVERT: C 875 ASP cc_start: 0.8869 (m-30) cc_final: 0.8353 (p0) REVERT: C 887 GLN cc_start: 0.9180 (tp40) cc_final: 0.8874 (tp-100) REVERT: C 901 LYS cc_start: 0.8719 (pttp) cc_final: 0.8212 (tptp) REVERT: C 912 HIS cc_start: 0.8328 (t70) cc_final: 0.7740 (t-90) REVERT: D 1281 ASN cc_start: 0.9321 (t0) cc_final: 0.8918 (t0) REVERT: D 1317 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8961 (ttmt) REVERT: E 690 MET cc_start: 0.8973 (mmm) cc_final: 0.8670 (tpp) REVERT: E 693 GLN cc_start: 0.9357 (tp40) cc_final: 0.8728 (tp40) REVERT: E 705 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8493 (tm-30) REVERT: E 720 MET cc_start: 0.8809 (mmt) cc_final: 0.8572 (mmm) REVERT: F 231 LYS cc_start: 0.9068 (tttt) cc_final: 0.8827 (ttmt) REVERT: F 250 ILE cc_start: 0.9713 (tp) cc_final: 0.9486 (mm) REVERT: F 274 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 279 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8226 (mtmt) REVERT: G 1045 ARG cc_start: 0.9297 (ptm160) cc_final: 0.8797 (ptm160) REVERT: G 1059 GLU cc_start: 0.8624 (tt0) cc_final: 0.8323 (tt0) REVERT: G 1077 LYS cc_start: 0.9377 (mmmt) cc_final: 0.9088 (mmmt) REVERT: G 1084 ARG cc_start: 0.8973 (tpt170) cc_final: 0.8498 (tpp80) REVERT: G 1087 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8650 (tp-100) REVERT: G 1088 LEU cc_start: 0.9325 (mm) cc_final: 0.9029 (mm) REVERT: H 1482 LYS cc_start: 0.9251 (mttt) cc_final: 0.8863 (mmtt) REVERT: H 1486 ILE cc_start: 0.9020 (mt) cc_final: 0.8715 (mt) REVERT: H 1490 GLU cc_start: 0.9053 (mp0) cc_final: 0.8838 (mp0) outliers start: 46 outliers final: 38 residues processed: 303 average time/residue: 0.1086 time to fit residues: 45.5162 Evaluate side-chains 312 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072022 restraints weight = 33584.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074270 restraints weight = 16351.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075752 restraints weight = 10888.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076659 restraints weight = 8635.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077187 restraints weight = 7590.334| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12230 Z= 0.155 Angle : 0.614 10.019 17678 Z= 0.359 Chirality : 0.035 0.177 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.105 174.321 3803 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.34 % Allowed : 32.69 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.18 (0.31), residues: 730 helix: 1.98 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.76 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1296 TYR 0.024 0.002 TYR D1318 PHE 0.012 0.001 PHE F 300 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00333 (12230) covalent geometry : angle 0.61424 (17678) hydrogen bonds : bond 0.03731 ( 746) hydrogen bonds : angle 2.95498 ( 1879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 304 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7865 (pp20) cc_final: 0.7422 (pp20) REVERT: A 460 LEU cc_start: 0.8420 (mm) cc_final: 0.7821 (mt) REVERT: A 468 GLN cc_start: 0.9023 (tt0) cc_final: 0.8331 (tm-30) REVERT: A 485 GLN cc_start: 0.8685 (mt0) cc_final: 0.8379 (mt0) REVERT: A 504 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8677 (m-10) REVERT: A 520 MET cc_start: 0.8138 (mtt) cc_final: 0.7593 (mtp) REVERT: A 525 GLN cc_start: 0.8867 (mt0) cc_final: 0.8406 (mp10) REVERT: B 35 ARG cc_start: 0.9012 (ttm-80) cc_final: 0.8375 (ttm110) REVERT: B 52 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8410 (tp30) REVERT: B 58 LEU cc_start: 0.9181 (tt) cc_final: 0.8922 (tt) REVERT: B 84 MET cc_start: 0.7937 (tpp) cc_final: 0.7606 (tpp) REVERT: B 88 TYR cc_start: 0.8419 (m-10) cc_final: 0.8168 (m-80) REVERT: B 92 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8304 (tmm-80) REVERT: C 821 GLN cc_start: 0.9064 (mp10) cc_final: 0.8779 (mp10) REVERT: C 822 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8767 (ttp80) REVERT: C 826 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8195 (mm-40) REVERT: C 853 TYR cc_start: 0.8693 (t80) cc_final: 0.8148 (t80) REVERT: C 875 ASP cc_start: 0.8806 (m-30) cc_final: 0.8313 (p0) REVERT: C 887 GLN cc_start: 0.9165 (tp40) cc_final: 0.8865 (tp-100) REVERT: C 900 ILE cc_start: 0.8471 (mp) cc_final: 0.8257 (mp) REVERT: C 901 LYS cc_start: 0.8627 (pttp) cc_final: 0.8093 (tptp) REVERT: C 912 HIS cc_start: 0.8262 (t70) cc_final: 0.7701 (t-90) REVERT: D 1279 HIS cc_start: 0.8786 (t-90) cc_final: 0.8454 (t70) REVERT: D 1281 ASN cc_start: 0.9266 (t0) cc_final: 0.8840 (t0) REVERT: D 1317 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8924 (ttmt) REVERT: E 668 GLN cc_start: 0.9026 (tt0) cc_final: 0.7895 (tm-30) REVERT: E 690 MET cc_start: 0.8826 (mmm) cc_final: 0.8556 (tpp) REVERT: E 693 GLN cc_start: 0.9332 (tp40) cc_final: 0.8754 (tp40) REVERT: E 705 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8497 (tm-30) REVERT: F 244 LYS cc_start: 0.9037 (tttt) cc_final: 0.8360 (tttt) REVERT: F 274 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8625 (tm-30) REVERT: F 279 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8302 (mtmt) REVERT: G 1045 ARG cc_start: 0.9264 (ptm160) cc_final: 0.8934 (ptm-80) REVERT: G 1059 GLU cc_start: 0.8543 (tt0) cc_final: 0.8302 (tt0) REVERT: G 1077 LYS cc_start: 0.9338 (mmmt) cc_final: 0.9077 (mmmt) REVERT: G 1079 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8660 (ptpp) REVERT: G 1084 ARG cc_start: 0.8961 (tpt170) cc_final: 0.8452 (tpp80) REVERT: G 1087 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8755 (tp-100) REVERT: G 1088 LEU cc_start: 0.9287 (mm) cc_final: 0.8956 (mm) REVERT: H 1432 GLU cc_start: 0.8193 (tp30) cc_final: 0.7817 (tp30) REVERT: H 1482 LYS cc_start: 0.9257 (mttt) cc_final: 0.8888 (mmtt) REVERT: H 1486 ILE cc_start: 0.8920 (mt) cc_final: 0.8648 (mt) REVERT: H 1490 GLU cc_start: 0.9028 (mp0) cc_final: 0.8815 (mp0) outliers start: 33 outliers final: 25 residues processed: 316 average time/residue: 0.1128 time to fit residues: 48.6446 Evaluate side-chains 313 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1073 SER Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072722 restraints weight = 33608.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074963 restraints weight = 16412.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076444 restraints weight = 10945.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077352 restraints weight = 8681.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077856 restraints weight = 7630.818| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 12230 Z= 0.165 Angle : 0.627 15.022 17678 Z= 0.362 Chirality : 0.035 0.187 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.102 174.090 3803 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.02 % Allowed : 35.11 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.24 (0.31), residues: 730 helix: 2.01 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 831 TYR 0.023 0.002 TYR D1318 PHE 0.023 0.002 PHE A 467 HIS 0.003 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00375 (12230) covalent geometry : angle 0.62673 (17678) hydrogen bonds : bond 0.03753 ( 746) hydrogen bonds : angle 3.02847 ( 1879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7913 (pp20) cc_final: 0.7243 (pm20) REVERT: A 468 GLN cc_start: 0.9071 (tt0) cc_final: 0.8442 (tm-30) REVERT: A 485 GLN cc_start: 0.8630 (mt0) cc_final: 0.8325 (mt0) REVERT: A 520 MET cc_start: 0.8079 (mtt) cc_final: 0.7659 (mtp) REVERT: B 35 ARG cc_start: 0.9015 (ttm-80) cc_final: 0.8397 (ttm110) REVERT: B 40 ARG cc_start: 0.9428 (tpp80) cc_final: 0.8881 (tpp80) REVERT: B 52 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8430 (tp30) REVERT: B 58 LEU cc_start: 0.9201 (tt) cc_final: 0.8928 (tt) REVERT: B 92 ARG cc_start: 0.8865 (tmm-80) cc_final: 0.8479 (ttt90) REVERT: C 821 GLN cc_start: 0.9138 (mp10) cc_final: 0.8836 (mp10) REVERT: C 822 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8697 (ttt90) REVERT: C 826 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8245 (mm-40) REVERT: C 853 TYR cc_start: 0.8648 (t80) cc_final: 0.8165 (t80) REVERT: C 875 ASP cc_start: 0.8820 (m-30) cc_final: 0.8323 (p0) REVERT: C 887 GLN cc_start: 0.9114 (tp40) cc_final: 0.8801 (tp-100) REVERT: C 901 LYS cc_start: 0.8570 (pttp) cc_final: 0.8015 (tptp) REVERT: C 912 HIS cc_start: 0.8255 (t70) cc_final: 0.7704 (t-90) REVERT: D 1279 HIS cc_start: 0.8825 (t-90) cc_final: 0.8483 (t70) REVERT: D 1281 ASN cc_start: 0.9163 (t0) cc_final: 0.8765 (t0) REVERT: D 1317 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8915 (ttmt) REVERT: E 690 MET cc_start: 0.8826 (mmm) cc_final: 0.8622 (tpp) REVERT: E 693 GLN cc_start: 0.9285 (tp40) cc_final: 0.8802 (tp40) REVERT: E 720 MET cc_start: 0.8842 (mmm) cc_final: 0.8464 (mmt) REVERT: F 274 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8533 (tm-30) REVERT: F 279 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8460 (mtpp) REVERT: G 1045 ARG cc_start: 0.9258 (ptm160) cc_final: 0.8762 (ptm160) REVERT: G 1059 GLU cc_start: 0.8539 (tt0) cc_final: 0.8262 (tt0) REVERT: G 1077 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9108 (mmmt) REVERT: G 1084 ARG cc_start: 0.8965 (tpt170) cc_final: 0.8445 (tpp80) REVERT: G 1087 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8727 (tp-100) REVERT: G 1088 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8927 (mm) REVERT: H 1432 GLU cc_start: 0.8014 (tp30) cc_final: 0.7808 (tp30) REVERT: H 1482 LYS cc_start: 0.9224 (mttt) cc_final: 0.8834 (mmtt) REVERT: H 1490 GLU cc_start: 0.9046 (mp0) cc_final: 0.8794 (mp0) outliers start: 31 outliers final: 21 residues processed: 307 average time/residue: 0.1153 time to fit residues: 48.5197 Evaluate side-chains 306 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.097144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070138 restraints weight = 33526.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.072267 restraints weight = 16595.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073702 restraints weight = 11129.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074591 restraints weight = 8836.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075089 restraints weight = 7747.593| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12230 Z= 0.236 Angle : 0.668 13.685 17678 Z= 0.384 Chirality : 0.037 0.202 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.201 173.730 3803 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.31 % Allowed : 35.44 % Favored : 58.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.11 (0.31), residues: 730 helix: 1.92 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.76 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.030 0.003 TYR B 88 PHE 0.017 0.002 PHE A 467 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00535 (12230) covalent geometry : angle 0.66773 (17678) hydrogen bonds : bond 0.04333 ( 746) hydrogen bonds : angle 3.31098 ( 1879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8171 (pp20) cc_final: 0.7019 (pm20) REVERT: A 468 GLN cc_start: 0.9181 (tt0) cc_final: 0.8617 (tm-30) REVERT: A 509 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9259 (mt) REVERT: A 520 MET cc_start: 0.8245 (mtt) cc_final: 0.7760 (mtp) REVERT: A 528 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8391 (ttp-170) REVERT: B 35 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8366 (ttm110) REVERT: B 52 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8597 (tp30) REVERT: B 84 MET cc_start: 0.8307 (tpp) cc_final: 0.7995 (tpp) REVERT: B 92 ARG cc_start: 0.8925 (tmm-80) cc_final: 0.8624 (ttt90) REVERT: B 97 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9167 (tp) REVERT: C 821 GLN cc_start: 0.9113 (mp10) cc_final: 0.8822 (mp10) REVERT: C 822 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8786 (ttp80) REVERT: C 853 TYR cc_start: 0.8602 (t80) cc_final: 0.8013 (t80) REVERT: C 875 ASP cc_start: 0.8833 (m-30) cc_final: 0.8330 (p0) REVERT: C 887 GLN cc_start: 0.9164 (tp40) cc_final: 0.8861 (tp-100) REVERT: C 901 LYS cc_start: 0.8710 (pttp) cc_final: 0.8250 (tptp) REVERT: C 912 HIS cc_start: 0.8302 (t70) cc_final: 0.7752 (t-90) REVERT: D 1279 HIS cc_start: 0.8880 (t-90) cc_final: 0.8651 (t-90) REVERT: D 1281 ASN cc_start: 0.9293 (t0) cc_final: 0.8856 (t0) REVERT: D 1317 LYS cc_start: 0.9254 (ttmm) cc_final: 0.8939 (ttmt) REVERT: E 668 GLN cc_start: 0.9100 (tt0) cc_final: 0.8033 (tm-30) REVERT: E 690 MET cc_start: 0.8943 (mmm) cc_final: 0.8656 (tpp) REVERT: E 693 GLN cc_start: 0.9379 (tp40) cc_final: 0.8834 (tp40) REVERT: E 705 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8586 (tm-30) REVERT: E 708 ASN cc_start: 0.9267 (t0) cc_final: 0.8918 (t0) REVERT: E 720 MET cc_start: 0.8779 (mmm) cc_final: 0.8552 (mmt) REVERT: F 244 LYS cc_start: 0.9014 (tttt) cc_final: 0.8476 (tttt) REVERT: F 274 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8546 (tm-30) REVERT: F 279 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8466 (mtpp) REVERT: G 1059 GLU cc_start: 0.8545 (tt0) cc_final: 0.8268 (tt0) REVERT: G 1077 LYS cc_start: 0.9367 (mmmt) cc_final: 0.9096 (mmmt) REVERT: G 1084 ARG cc_start: 0.8992 (tpt170) cc_final: 0.8478 (tpp80) REVERT: G 1087 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8749 (tp-100) REVERT: G 1088 LEU cc_start: 0.9303 (mm) cc_final: 0.8980 (mm) REVERT: H 1482 LYS cc_start: 0.9213 (mttt) cc_final: 0.8789 (mmtt) REVERT: H 1490 GLU cc_start: 0.9042 (mp0) cc_final: 0.8807 (mp0) outliers start: 39 outliers final: 31 residues processed: 297 average time/residue: 0.1071 time to fit residues: 43.8296 Evaluate side-chains 307 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain H residue 1433 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071695 restraints weight = 32902.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.073855 restraints weight = 16423.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075309 restraints weight = 11067.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076197 restraints weight = 8815.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076671 restraints weight = 7758.414| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12230 Z= 0.178 Angle : 0.660 12.359 17678 Z= 0.378 Chirality : 0.036 0.246 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.089 174.050 3803 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.18 % Allowed : 37.22 % Favored : 57.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.07 (0.31), residues: 730 helix: 1.87 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.70 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 831 TYR 0.025 0.002 TYR D1318 PHE 0.017 0.002 PHE A 467 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00402 (12230) covalent geometry : angle 0.65994 (17678) hydrogen bonds : bond 0.03941 ( 746) hydrogen bonds : angle 3.20327 ( 1879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8049 (pp20) cc_final: 0.6771 (pm20) REVERT: A 468 GLN cc_start: 0.9092 (tt0) cc_final: 0.8532 (tm-30) REVERT: A 485 GLN cc_start: 0.8709 (mt0) cc_final: 0.8379 (mt0) REVERT: A 520 MET cc_start: 0.8182 (mtt) cc_final: 0.7671 (mtp) REVERT: A 528 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8243 (ttp-170) REVERT: B 35 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8382 (ttm110) REVERT: B 52 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8500 (tp30) REVERT: B 58 LEU cc_start: 0.9181 (tt) cc_final: 0.8948 (tt) REVERT: B 88 TYR cc_start: 0.7665 (m-80) cc_final: 0.7177 (m-80) REVERT: B 92 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8534 (ttt90) REVERT: C 821 GLN cc_start: 0.9117 (mp10) cc_final: 0.8818 (mp10) REVERT: C 822 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8744 (ttt90) REVERT: C 826 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8169 (mm-40) REVERT: C 853 TYR cc_start: 0.8517 (t80) cc_final: 0.8031 (t80) REVERT: C 875 ASP cc_start: 0.8825 (m-30) cc_final: 0.8318 (p0) REVERT: C 887 GLN cc_start: 0.9140 (tp40) cc_final: 0.8838 (tp-100) REVERT: C 901 LYS cc_start: 0.8638 (pttp) cc_final: 0.8098 (tptp) REVERT: C 912 HIS cc_start: 0.8299 (t70) cc_final: 0.7779 (t-90) REVERT: D 1279 HIS cc_start: 0.8879 (t-90) cc_final: 0.8496 (t-170) REVERT: D 1281 ASN cc_start: 0.9267 (t0) cc_final: 0.8830 (t0) REVERT: D 1317 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8905 (ttmt) REVERT: E 685 GLN cc_start: 0.8468 (mt0) cc_final: 0.8268 (mt0) REVERT: E 690 MET cc_start: 0.8874 (mmm) cc_final: 0.8663 (tpp) REVERT: E 693 GLN cc_start: 0.9313 (tp40) cc_final: 0.8820 (tp40) REVERT: E 708 ASN cc_start: 0.9256 (t0) cc_final: 0.8933 (t0) REVERT: E 720 MET cc_start: 0.8780 (mmm) cc_final: 0.8577 (mmt) REVERT: F 244 LYS cc_start: 0.9024 (tttt) cc_final: 0.8356 (tttt) REVERT: F 274 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8502 (tm-30) REVERT: F 279 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8498 (mtpp) REVERT: G 1059 GLU cc_start: 0.8512 (tt0) cc_final: 0.8247 (tt0) REVERT: G 1077 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9092 (mmmt) REVERT: G 1084 ARG cc_start: 0.8969 (tpt170) cc_final: 0.8428 (tpp80) REVERT: G 1087 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8748 (tp-100) REVERT: G 1088 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8950 (mm) REVERT: H 1482 LYS cc_start: 0.9211 (mttt) cc_final: 0.8796 (mmtt) REVERT: H 1490 GLU cc_start: 0.9065 (mp0) cc_final: 0.8811 (mp0) outliers start: 32 outliers final: 25 residues processed: 300 average time/residue: 0.1125 time to fit residues: 46.5756 Evaluate side-chains 311 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 GLN E 655 GLN E 668 GLN ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072074 restraints weight = 35167.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074408 restraints weight = 17220.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075982 restraints weight = 11468.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.076947 restraints weight = 9035.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077466 restraints weight = 7894.542| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12230 Z= 0.207 Angle : 0.670 11.759 17678 Z= 0.384 Chirality : 0.036 0.203 2019 Planarity : 0.005 0.052 1290 Dihedral : 31.082 173.713 3803 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.18 % Allowed : 38.35 % Favored : 56.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.99 (0.30), residues: 730 helix: 1.82 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.73 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 831 TYR 0.026 0.002 TYR D1318 PHE 0.025 0.002 PHE A 467 HIS 0.003 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00474 (12230) covalent geometry : angle 0.67037 (17678) hydrogen bonds : bond 0.04167 ( 746) hydrogen bonds : angle 3.30707 ( 1879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7966 (pp20) cc_final: 0.6766 (pm20) REVERT: A 468 GLN cc_start: 0.9150 (tt0) cc_final: 0.8586 (tm-30) REVERT: A 520 MET cc_start: 0.8204 (mtt) cc_final: 0.7692 (mtp) REVERT: B 35 ARG cc_start: 0.9024 (ttm-80) cc_final: 0.8380 (ttm110) REVERT: B 52 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8544 (tp30) REVERT: B 58 LEU cc_start: 0.9199 (tt) cc_final: 0.8959 (tt) REVERT: B 88 TYR cc_start: 0.7648 (m-80) cc_final: 0.7077 (m-80) REVERT: B 92 ARG cc_start: 0.8946 (tmm-80) cc_final: 0.8569 (ttt90) REVERT: C 821 GLN cc_start: 0.9127 (mp10) cc_final: 0.8826 (mp10) REVERT: C 822 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8749 (ttt90) REVERT: C 853 TYR cc_start: 0.8499 (t80) cc_final: 0.8053 (t80) REVERT: C 875 ASP cc_start: 0.8821 (m-30) cc_final: 0.8334 (p0) REVERT: C 887 GLN cc_start: 0.9136 (tp40) cc_final: 0.8840 (tp-100) REVERT: C 901 LYS cc_start: 0.8643 (pttp) cc_final: 0.8187 (tptp) REVERT: C 912 HIS cc_start: 0.8326 (t70) cc_final: 0.7742 (t-90) REVERT: D 1279 HIS cc_start: 0.8877 (t-90) cc_final: 0.8497 (t-170) REVERT: D 1281 ASN cc_start: 0.9262 (t0) cc_final: 0.8822 (t0) REVERT: D 1317 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8927 (ttmt) REVERT: E 668 GLN cc_start: 0.9104 (tt0) cc_final: 0.7985 (tm-30) REVERT: E 690 MET cc_start: 0.8899 (mmm) cc_final: 0.8695 (tpp) REVERT: E 693 GLN cc_start: 0.9315 (tp40) cc_final: 0.8805 (tp40) REVERT: E 708 ASN cc_start: 0.9271 (t0) cc_final: 0.8896 (t0) REVERT: F 244 LYS cc_start: 0.9011 (tttt) cc_final: 0.8373 (tttt) REVERT: F 274 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8481 (tm-30) REVERT: F 279 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8456 (mtpp) REVERT: G 1059 GLU cc_start: 0.8527 (tt0) cc_final: 0.8254 (tt0) REVERT: G 1077 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9060 (mmmt) REVERT: G 1084 ARG cc_start: 0.8984 (tpt170) cc_final: 0.8456 (tpp80) REVERT: G 1087 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8716 (tp-100) REVERT: G 1088 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8982 (mm) REVERT: H 1482 LYS cc_start: 0.9212 (mttt) cc_final: 0.8776 (mmtt) REVERT: H 1490 GLU cc_start: 0.9058 (mp0) cc_final: 0.8812 (mp0) outliers start: 32 outliers final: 28 residues processed: 289 average time/residue: 0.1064 time to fit residues: 42.3020 Evaluate side-chains 302 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1087 GLN Chi-restraints excluded: chain G residue 1088 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072783 restraints weight = 34870.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075132 restraints weight = 17104.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076684 restraints weight = 11407.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.077661 restraints weight = 9011.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078169 restraints weight = 7873.479| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12230 Z= 0.186 Angle : 0.668 12.161 17678 Z= 0.380 Chirality : 0.036 0.204 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.038 173.915 3803 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.50 % Allowed : 37.86 % Favored : 56.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.04 (0.31), residues: 730 helix: 1.87 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.75 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 534 TYR 0.024 0.002 TYR D1318 PHE 0.022 0.002 PHE A 467 HIS 0.004 0.001 HIS E 713 Details of bonding type rmsd covalent geometry : bond 0.00425 (12230) covalent geometry : angle 0.66767 (17678) hydrogen bonds : bond 0.04056 ( 746) hydrogen bonds : angle 3.24702 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.58 seconds wall clock time: 32 minutes 13.06 seconds (1933.06 seconds total)