Starting phenix.real_space_refine on Tue Jul 29 10:26:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m1x_23626/07_2025/7m1x_23626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1x_23626/07_2025/7m1x_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_23626/07_2025/7m1x_23626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2025/7m1x_23626.map" model { file = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2025/7m1x_23626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1x_23626/07_2025/7m1x_23626.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.32, per 1000 atoms: 0.64 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: 2.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.90 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: 8.58 Time building geometry restraints manager: 3.32 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: 0.630 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- 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 : 6.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (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 HIS 0.005 0.001 HIS F 275 PHE 0.018 0.002 PHE A 478 TYR 0.015 0.002 TYR C 860 ARG 0.005 0.000 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.09819 ( 746) hydrogen bonds : angle 4.08767 ( 1879) covalent geometry : bond 0.00698 (12230) covalent geometry : angle 0.77919 (17678) *********************** 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 : 0.810 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: 0.8775 (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: 0.8746 (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: 0.8839 (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: 0.8486 (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: 0.9426 (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: 0.8932 (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: 0.8511 (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: 0.8850 (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: 0.2932 time to fit residues: 136.7736 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 : 0.819 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1446 HIS H1481 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.071980 restraints weight = 33043.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074226 restraints weight = 15882.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075730 restraints weight = 10514.630| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1878 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= 0.153 Angle : 0.610 7.179 17678 Z= 0.357 Chirality : 0.035 0.152 2019 Planarity : 0.004 0.054 1290 Dihedral : 31.405 174.528 3809 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.05 % Allowed : 23.95 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 730 helix: 1.34 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.94 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 667 TYR 0.020 0.002 TYR D1318 ARG 0.010 0.001 ARG C 845 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 746) hydrogen bonds : angle 3.05487 ( 1879) covalent geometry : bond 0.00329 (12230) covalent geometry : angle 0.61004 (17678) *********************** 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 348 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.8980 (tt0) cc_final: 0.8367 (tm-30) REVERT: A 473 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 485 GLN cc_start: 0.8728 (mt0) cc_final: 0.8319 (mt0) REVERT: A 520 MET cc_start: 0.8052 (mtt) cc_final: 0.7600 (mtp) REVERT: B 52 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8346 (tp30) REVERT: B 81 VAL cc_start: 0.9347 (t) cc_final: 0.8984 (p) REVERT: B 92 ARG cc_start: 0.8748 (tmm-80) cc_final: 0.8003 (tmm-80) REVERT: C 822 ARG cc_start: 0.9086 (ttp80) cc_final: 0.8817 (ttt-90) REVERT: C 837 LYS cc_start: 0.8881 (tppt) cc_final: 0.8634 (ttpp) REVERT: C 853 TYR cc_start: 0.8751 (t80) cc_final: 0.8177 (t80) REVERT: C 867 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8600 (tm-30) REVERT: C 875 ASP cc_start: 0.8834 (m-30) cc_final: 0.8300 (p0) REVERT: C 884 ARG cc_start: 0.8929 (tpt170) cc_final: 0.8669 (tpt170) REVERT: C 887 GLN cc_start: 0.9175 (tp40) cc_final: 0.8857 (tp-100) REVERT: C 901 LYS cc_start: 0.8871 (pttp) cc_final: 0.8273 (tptp) REVERT: C 912 HIS cc_start: 0.8274 (t70) cc_final: 0.7710 (t-90) REVERT: D 1243 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8341 (mmmt) REVERT: D 1268 GLU cc_start: 0.8940 (tp30) cc_final: 0.8721 (tp30) REVERT: D 1279 HIS cc_start: 0.8666 (t-90) cc_final: 0.8016 (t70) REVERT: D 1281 ASN cc_start: 0.9307 (t0) cc_final: 0.8902 (t0) REVERT: D 1317 LYS cc_start: 0.9324 (ttmm) cc_final: 0.8974 (ttmt) REVERT: E 705 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8505 (tm-30) REVERT: E 720 MET cc_start: 0.8790 (tpp) cc_final: 0.8355 (mmm) REVERT: E 725 GLN cc_start: 0.9174 (mt0) cc_final: 0.8894 (mt0) REVERT: F 231 LYS cc_start: 0.8830 (tttt) cc_final: 0.8614 (ttmt) REVERT: F 244 LYS cc_start: 0.9089 (tttt) cc_final: 0.8738 (tttt) REVERT: F 249 LEU cc_start: 0.9216 (mt) cc_final: 0.8798 (mt) REVERT: F 252 GLU cc_start: 0.8727 (mp0) cc_final: 0.8409 (pm20) REVERT: F 274 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8737 (tm-30) REVERT: F 284 MET cc_start: 0.8907 (tpp) cc_final: 0.8313 (mmm) REVERT: F 291 LYS cc_start: 0.9021 (tttp) cc_final: 0.8621 (ttpt) REVERT: G 1059 GLU cc_start: 0.8662 (tt0) cc_final: 0.8409 (tt0) REVERT: G 1084 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8444 (tpp80) REVERT: G 1088 LEU cc_start: 0.9288 (mm) cc_final: 0.8949 (mm) REVERT: H 1433 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (m) REVERT: H 1461 SER cc_start: 0.9483 (t) cc_final: 0.9257 (t) REVERT: H 1465 ASP cc_start: 0.9216 (t70) cc_final: 0.8921 (t0) REVERT: H 1468 GLU cc_start: 0.8575 (tp30) cc_final: 0.8322 (tt0) REVERT: H 1469 ARG cc_start: 0.9246 (ttm170) cc_final: 0.9021 (mtm180) REVERT: H 1486 ILE cc_start: 0.8964 (mt) cc_final: 0.8608 (mt) outliers start: 25 outliers final: 15 residues processed: 330 average time/residue: 0.3001 time to fit residues: 131.6027 Evaluate side-chains 302 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 286 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 C residue 886 LEU 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 297 LEU Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain H residue 1433 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 E 655 GLN E 668 GLN G1033 HIS ** G1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.071550 restraints weight = 32250.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073765 restraints weight = 15418.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075244 restraints weight = 10258.850| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2363 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= 0.167 Angle : 0.595 8.223 17678 Z= 0.351 Chirality : 0.034 0.161 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.301 174.299 3805 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.02 % Allowed : 28.48 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.30), residues: 730 helix: 1.85 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.76 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.012 0.001 PHE E 667 TYR 0.022 0.002 TYR D1318 ARG 0.007 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 746) hydrogen bonds : angle 3.00296 ( 1879) covalent geometry : bond 0.00366 (12230) covalent geometry : angle 0.59525 (17678) *********************** 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 339 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8012 (pp20) cc_final: 0.7695 (pp20) REVERT: A 460 LEU cc_start: 0.8538 (mm) cc_final: 0.8003 (tp) REVERT: A 467 PHE cc_start: 0.8946 (t80) cc_final: 0.8746 (t80) REVERT: A 468 GLN cc_start: 0.9038 (tt0) cc_final: 0.8790 (tm-30) REVERT: A 473 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 520 MET cc_start: 0.8205 (mtt) cc_final: 0.7628 (mtp) REVERT: A 534 ARG cc_start: 0.8178 (ptp-110) cc_final: 0.7977 (ptp-110) REVERT: B 52 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8540 (tp30) REVERT: B 81 VAL cc_start: 0.9306 (t) cc_final: 0.8988 (p) REVERT: B 92 ARG cc_start: 0.8783 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: C 821 GLN cc_start: 0.9137 (mp10) cc_final: 0.8827 (mp10) REVERT: C 822 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8829 (ttt-90) REVERT: C 853 TYR cc_start: 0.8771 (t80) cc_final: 0.8120 (t80) REVERT: C 867 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8764 (tm-30) REVERT: C 875 ASP cc_start: 0.8829 (m-30) cc_final: 0.8330 (p0) REVERT: C 884 ARG cc_start: 0.8852 (tpt170) cc_final: 0.8584 (tpt170) REVERT: C 887 GLN cc_start: 0.9121 (tp40) cc_final: 0.8823 (tp-100) REVERT: C 901 LYS cc_start: 0.8897 (pttp) cc_final: 0.8422 (tptp) REVERT: C 912 HIS cc_start: 0.8362 (t70) cc_final: 0.7781 (t-90) REVERT: D 1268 GLU cc_start: 0.9028 (tp30) cc_final: 0.8755 (tp30) REVERT: D 1281 ASN cc_start: 0.9286 (t0) cc_final: 0.8891 (t0) REVERT: D 1317 LYS cc_start: 0.9325 (ttmm) cc_final: 0.8978 (ttmt) REVERT: E 693 GLN cc_start: 0.9244 (tp40) cc_final: 0.8941 (tp40) REVERT: E 705 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8473 (tm-30) REVERT: E 708 ASN cc_start: 0.9333 (t0) cc_final: 0.9046 (t0) REVERT: E 720 MET cc_start: 0.8869 (tpp) cc_final: 0.8506 (mmm) REVERT: E 725 GLN cc_start: 0.9159 (mt0) cc_final: 0.8902 (mt0) REVERT: F 231 LYS cc_start: 0.8962 (tttt) cc_final: 0.8753 (ttmt) REVERT: F 244 LYS cc_start: 0.9186 (tttt) cc_final: 0.8638 (tttt) REVERT: F 249 LEU cc_start: 0.9206 (mt) cc_final: 0.8948 (mt) REVERT: F 252 GLU cc_start: 0.8777 (mp0) cc_final: 0.8517 (pm20) REVERT: F 274 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8596 (tm-30) REVERT: F 277 LYS cc_start: 0.9488 (mttm) cc_final: 0.9192 (mmtp) REVERT: F 284 MET cc_start: 0.8891 (tpp) cc_final: 0.8661 (tpp) REVERT: F 291 LYS cc_start: 0.9043 (tttp) cc_final: 0.8815 (tttt) REVERT: G 1021 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: G 1045 ARG cc_start: 0.9373 (ptm160) cc_final: 0.9046 (ptm160) REVERT: G 1077 LYS cc_start: 0.9309 (mmmt) cc_final: 0.9109 (mmmt) REVERT: G 1079 LYS cc_start: 0.9237 (ttmm) cc_final: 0.9004 (ttpt) REVERT: G 1084 ARG cc_start: 0.8935 (tpt170) cc_final: 0.8429 (tpp80) REVERT: G 1087 GLN cc_start: 0.9009 (tp40) cc_final: 0.8618 (tp40) REVERT: G 1088 LEU cc_start: 0.9265 (mm) cc_final: 0.8915 (mm) REVERT: H 1468 GLU cc_start: 0.8585 (tp30) cc_final: 0.8354 (tt0) REVERT: H 1469 ARG cc_start: 0.9251 (ttm170) cc_final: 0.8926 (mtm180) REVERT: H 1486 ILE cc_start: 0.8982 (mt) cc_final: 0.8667 (mt) outliers start: 31 outliers final: 22 residues processed: 318 average time/residue: 0.2802 time to fit residues: 120.8507 Evaluate side-chains 309 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 496 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN 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 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 1021 GLN Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain H residue 1508 VAL Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.099158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.071972 restraints weight = 33325.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074203 restraints weight = 16365.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075675 restraints weight = 10942.062| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12230 Z= 0.158 Angle : 0.591 7.968 17678 Z= 0.349 Chirality : 0.034 0.168 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.147 174.215 3803 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.37 % Allowed : 31.39 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 730 helix: 2.00 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.008 0.001 PHE B 100 TYR 0.022 0.002 TYR D1318 ARG 0.005 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 746) hydrogen bonds : angle 2.94645 ( 1879) covalent geometry : bond 0.00348 (12230) covalent geometry : angle 0.59122 (17678) *********************** 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 330 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7998 (pp20) cc_final: 0.7666 (pp20) REVERT: A 460 LEU cc_start: 0.8448 (mm) cc_final: 0.7961 (mt) REVERT: A 473 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 485 GLN cc_start: 0.8637 (mt0) cc_final: 0.8434 (mt0) REVERT: B 35 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8506 (ttm110) REVERT: B 52 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8497 (tp30) REVERT: B 92 ARG cc_start: 0.8818 (tmm-80) cc_final: 0.8305 (tmm-80) REVERT: C 821 GLN cc_start: 0.9117 (mp10) cc_final: 0.8798 (mp10) REVERT: C 822 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8768 (ttt-90) REVERT: C 826 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8163 (mm-40) REVERT: C 853 TYR cc_start: 0.8663 (t80) cc_final: 0.7994 (t80) REVERT: C 867 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8741 (tm-30) REVERT: C 875 ASP cc_start: 0.8818 (m-30) cc_final: 0.8311 (p0) REVERT: C 879 LYS cc_start: 0.8935 (mttt) cc_final: 0.8321 (mtmt) REVERT: C 884 ARG cc_start: 0.8824 (tpt170) cc_final: 0.8561 (tpt170) REVERT: C 887 GLN cc_start: 0.9129 (tp40) cc_final: 0.8854 (tp-100) REVERT: C 901 LYS cc_start: 0.8781 (pttp) cc_final: 0.8331 (tptp) REVERT: C 912 HIS cc_start: 0.8272 (t70) cc_final: 0.7811 (t-90) REVERT: D 1268 GLU cc_start: 0.8997 (tp30) cc_final: 0.8629 (tp30) REVERT: D 1279 HIS cc_start: 0.8834 (t-90) cc_final: 0.8446 (t-170) REVERT: D 1281 ASN cc_start: 0.9212 (t0) cc_final: 0.8808 (t0) REVERT: D 1317 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8960 (ttmt) REVERT: E 693 GLN cc_start: 0.9285 (tp40) cc_final: 0.8832 (tp40) REVERT: E 705 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 231 LYS cc_start: 0.9034 (tttt) cc_final: 0.8778 (ttmt) REVERT: F 244 LYS cc_start: 0.9109 (tttt) cc_final: 0.8838 (tttt) REVERT: F 247 SER cc_start: 0.8789 (p) cc_final: 0.8540 (t) REVERT: F 274 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8541 (tm-30) REVERT: F 277 LYS cc_start: 0.9473 (mttm) cc_final: 0.9174 (mmtp) REVERT: F 291 LYS cc_start: 0.9027 (tttp) cc_final: 0.8815 (tttt) REVERT: G 1031 ARG cc_start: 0.8805 (ttm170) cc_final: 0.8589 (ttm170) REVERT: G 1045 ARG cc_start: 0.9343 (ptm160) cc_final: 0.8968 (ptm160) REVERT: G 1077 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9059 (mmmt) REVERT: G 1079 LYS cc_start: 0.9249 (ttmm) cc_final: 0.9029 (ttpt) REVERT: G 1084 ARG cc_start: 0.8899 (tpt170) cc_final: 0.8177 (tpp80) REVERT: G 1088 LEU cc_start: 0.9182 (mm) cc_final: 0.8836 (mm) REVERT: H 1468 GLU cc_start: 0.8565 (tp30) cc_final: 0.8319 (tt0) REVERT: H 1490 GLU cc_start: 0.9156 (mp0) cc_final: 0.8907 (mp0) outliers start: 27 outliers final: 21 residues processed: 311 average time/residue: 0.2722 time to fit residues: 114.5083 Evaluate side-chains 311 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 882 THR 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 1275 SER Chi-restraints excluded: chain D residue 1277 LEU 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 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1073 SER Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.100666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073976 restraints weight = 33176.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076184 restraints weight = 16152.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077680 restraints weight = 10775.144| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2854 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= 0.157 Angle : 0.601 14.002 17678 Z= 0.350 Chirality : 0.034 0.190 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.082 174.151 3803 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.21 % Allowed : 33.01 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 730 helix: 2.05 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.52 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.023 0.001 PHE A 467 TYR 0.023 0.002 TYR B 88 ARG 0.006 0.000 ARG G1034 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 746) hydrogen bonds : angle 2.92469 ( 1879) covalent geometry : bond 0.00346 (12230) covalent geometry : angle 0.60076 (17678) *********************** 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 321 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.806 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: 0.7974 (pp20) cc_final: 0.7311 (pp20) REVERT: A 460 LEU cc_start: 0.8385 (mm) cc_final: 0.7597 (mt) REVERT: A 468 GLN cc_start: 0.8947 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 473 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 485 GLN cc_start: 0.8604 (mt0) cc_final: 0.8350 (mt0) REVERT: A 525 GLN cc_start: 0.8890 (mt0) cc_final: 0.8407 (mp10) REVERT: B 35 ARG cc_start: 0.9106 (ttm-80) cc_final: 0.8449 (ttm110) REVERT: B 52 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8499 (tp30) REVERT: B 58 LEU cc_start: 0.9258 (tt) cc_final: 0.9035 (tt) REVERT: B 88 TYR cc_start: 0.8011 (m-80) cc_final: 0.7525 (m-80) REVERT: B 92 ARG cc_start: 0.8804 (tmm-80) cc_final: 0.8303 (tmm-80) REVERT: C 821 GLN cc_start: 0.9134 (mp10) cc_final: 0.8811 (mp10) REVERT: C 822 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8723 (ttt-90) REVERT: C 853 TYR cc_start: 0.8573 (t80) cc_final: 0.8117 (t80) REVERT: C 867 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8713 (tm-30) REVERT: C 875 ASP cc_start: 0.8811 (m-30) cc_final: 0.8310 (p0) REVERT: C 879 LYS cc_start: 0.8948 (mttt) cc_final: 0.8328 (mtmt) REVERT: C 887 GLN cc_start: 0.9164 (tp40) cc_final: 0.8885 (tp-100) REVERT: C 901 LYS cc_start: 0.8675 (pttp) cc_final: 0.8241 (tptp) REVERT: C 912 HIS cc_start: 0.8272 (t70) cc_final: 0.7744 (t-90) REVERT: D 1268 GLU cc_start: 0.8978 (tp30) cc_final: 0.8621 (tp30) REVERT: D 1279 HIS cc_start: 0.8899 (t-90) cc_final: 0.8506 (t-170) REVERT: D 1281 ASN cc_start: 0.9184 (t0) cc_final: 0.8790 (t0) REVERT: D 1317 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8941 (ttmt) REVERT: E 653 ARG cc_start: 0.8730 (tpt170) cc_final: 0.8495 (tpt170) REVERT: E 668 GLN cc_start: 0.9026 (tt0) cc_final: 0.8085 (tm-30) REVERT: E 693 GLN cc_start: 0.9307 (tp40) cc_final: 0.8951 (tp40) REVERT: E 705 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 720 MET cc_start: 0.8844 (mmm) cc_final: 0.8571 (mmt) REVERT: F 231 LYS cc_start: 0.9078 (tttt) cc_final: 0.8866 (ttmt) REVERT: F 274 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8536 (tm-30) REVERT: F 277 LYS cc_start: 0.9470 (mttm) cc_final: 0.9185 (mmtp) REVERT: F 291 LYS cc_start: 0.9073 (tttp) cc_final: 0.8835 (tttt) REVERT: G 1026 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8069 (mp10) REVERT: G 1031 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8524 (ttm170) REVERT: G 1077 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9054 (mmmt) REVERT: G 1084 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8178 (tpp80) REVERT: G 1088 LEU cc_start: 0.9203 (mm) cc_final: 0.8900 (mm) REVERT: H 1432 GLU cc_start: 0.8103 (tp30) cc_final: 0.7866 (tp30) REVERT: H 1482 LYS cc_start: 0.9213 (mttt) cc_final: 0.8851 (mmtt) REVERT: H 1490 GLU cc_start: 0.9043 (mp0) cc_final: 0.8831 (mp0) outliers start: 26 outliers final: 22 residues processed: 303 average time/residue: 0.2883 time to fit residues: 119.5585 Evaluate side-chains 308 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 C residue 861 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1277 LEU 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 717 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1020 SER Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1073 SER 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 75 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.100675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.073288 restraints weight = 33396.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075493 restraints weight = 16369.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077008 restraints weight = 10904.636| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12230 Z= 0.157 Angle : 0.596 8.963 17678 Z= 0.349 Chirality : 0.035 0.177 2019 Planarity : 0.004 0.050 1290 Dihedral : 31.049 174.077 3803 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.53 % Allowed : 32.36 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 730 helix: 2.05 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.47 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.008 0.001 PHE D1267 TYR 0.024 0.002 TYR D1318 ARG 0.005 0.000 ARG G1034 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 746) hydrogen bonds : angle 2.88276 ( 1879) covalent geometry : bond 0.00344 (12230) covalent geometry : angle 0.59601 (17678) *********************** 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 320 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7949 (pp20) cc_final: 0.7297 (pp20) REVERT: A 460 LEU cc_start: 0.8376 (mm) cc_final: 0.7664 (mt) REVERT: A 468 GLN cc_start: 0.8982 (tt0) cc_final: 0.8607 (tm-30) REVERT: A 473 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 485 GLN cc_start: 0.8592 (mt0) cc_final: 0.8295 (mt0) REVERT: A 494 GLU cc_start: 0.8725 (tp30) cc_final: 0.8515 (tp30) REVERT: A 525 GLN cc_start: 0.8840 (mt0) cc_final: 0.8336 (mp10) REVERT: B 35 ARG cc_start: 0.9088 (ttm-80) cc_final: 0.8484 (ttm110) REVERT: B 58 LEU cc_start: 0.9227 (tt) cc_final: 0.8981 (tt) REVERT: B 88 TYR cc_start: 0.8062 (m-80) cc_final: 0.7782 (m-80) REVERT: B 92 ARG cc_start: 0.8844 (tmm-80) cc_final: 0.8326 (tmm-80) REVERT: C 821 GLN cc_start: 0.9100 (mp10) cc_final: 0.8773 (mp10) REVERT: C 822 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8642 (ttp80) REVERT: C 853 TYR cc_start: 0.8615 (t80) cc_final: 0.8166 (t80) REVERT: C 867 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8748 (tm-30) REVERT: C 875 ASP cc_start: 0.8855 (m-30) cc_final: 0.8326 (p0) REVERT: C 879 LYS cc_start: 0.8939 (mttt) cc_final: 0.8316 (mtmt) REVERT: C 887 GLN cc_start: 0.9111 (tp40) cc_final: 0.8828 (tp-100) REVERT: C 901 LYS cc_start: 0.8638 (pttp) cc_final: 0.8176 (tptp) REVERT: C 912 HIS cc_start: 0.8326 (t70) cc_final: 0.7786 (t-90) REVERT: D 1268 GLU cc_start: 0.9017 (tp30) cc_final: 0.8599 (tp30) REVERT: D 1279 HIS cc_start: 0.8928 (t-90) cc_final: 0.8487 (t-170) REVERT: D 1281 ASN cc_start: 0.9135 (t0) cc_final: 0.8775 (t0) REVERT: D 1317 LYS cc_start: 0.9266 (ttmm) cc_final: 0.8929 (ttmt) REVERT: E 653 ARG cc_start: 0.8765 (tpt170) cc_final: 0.8507 (tpt170) REVERT: E 693 GLN cc_start: 0.9286 (tp40) cc_final: 0.8851 (tp40) REVERT: E 705 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8504 (tm-30) REVERT: F 231 LYS cc_start: 0.9075 (tttt) cc_final: 0.8621 (ttmt) REVERT: F 274 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8557 (tm-30) REVERT: F 284 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8528 (tpp) REVERT: F 291 LYS cc_start: 0.9014 (tttp) cc_final: 0.8600 (ttpt) REVERT: G 1077 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9091 (mmmt) REVERT: G 1079 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8856 (ttpp) REVERT: G 1084 ARG cc_start: 0.8944 (tpt170) cc_final: 0.8218 (tpp80) REVERT: G 1088 LEU cc_start: 0.9176 (mm) cc_final: 0.8871 (mm) REVERT: H 1482 LYS cc_start: 0.9205 (mttt) cc_final: 0.8841 (mmtt) REVERT: H 1490 GLU cc_start: 0.9016 (mp0) cc_final: 0.8769 (mp0) outliers start: 28 outliers final: 22 residues processed: 301 average time/residue: 0.2873 time to fit residues: 116.5781 Evaluate side-chains 304 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 D residue 1241 VAL Chi-restraints excluded: chain D residue 1277 LEU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 658 THR 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 724 ILE Chi-restraints excluded: chain F residue 284 MET 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 1073 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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** ** 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 = 0.3797 r_free = 0.3797 target = 0.097599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070636 restraints weight = 33802.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072796 restraints weight = 16591.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074252 restraints weight = 11074.499| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 12230 Z= 0.238 Angle : 0.648 9.060 17678 Z= 0.375 Chirality : 0.036 0.189 2019 Planarity : 0.004 0.050 1290 Dihedral : 31.205 173.799 3803 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.80 % Allowed : 31.55 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.31), residues: 730 helix: 1.86 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.52 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 275 PHE 0.030 0.002 PHE A 467 TYR 0.049 0.003 TYR D1237 ARG 0.006 0.001 ARG C 831 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 746) hydrogen bonds : angle 3.25748 ( 1879) covalent geometry : bond 0.00543 (12230) covalent geometry : angle 0.64769 (17678) *********************** 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 324 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.917 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: 0.7982 (pp20) cc_final: 0.7397 (pp20) REVERT: A 460 LEU cc_start: 0.8462 (mm) cc_final: 0.7619 (mt) REVERT: A 473 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 485 GLN cc_start: 0.8799 (mt0) cc_final: 0.8514 (mt0) REVERT: A 525 GLN cc_start: 0.8840 (mt0) cc_final: 0.8391 (mp10) REVERT: B 35 ARG cc_start: 0.9100 (ttm-80) cc_final: 0.8434 (ttm110) REVERT: B 53 GLU cc_start: 0.9348 (tp30) cc_final: 0.9004 (tp30) REVERT: B 88 TYR cc_start: 0.8248 (m-80) cc_final: 0.7852 (m-80) REVERT: B 92 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8287 (tmm-80) REVERT: C 821 GLN cc_start: 0.9113 (mp10) cc_final: 0.8796 (mp10) REVERT: C 822 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8790 (ttt-90) REVERT: C 853 TYR cc_start: 0.8611 (t80) cc_final: 0.8187 (t80) REVERT: C 867 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8774 (tm-30) REVERT: C 875 ASP cc_start: 0.8862 (m-30) cc_final: 0.8344 (p0) REVERT: C 879 LYS cc_start: 0.8957 (mttt) cc_final: 0.8374 (mtmt) REVERT: C 887 GLN cc_start: 0.9213 (tp40) cc_final: 0.8929 (tp-100) REVERT: C 901 LYS cc_start: 0.8704 (pttp) cc_final: 0.8174 (tptp) REVERT: C 912 HIS cc_start: 0.8332 (t70) cc_final: 0.7764 (t-90) REVERT: D 1268 GLU cc_start: 0.9039 (tp30) cc_final: 0.8571 (tp30) REVERT: D 1279 HIS cc_start: 0.8820 (t-90) cc_final: 0.8493 (t70) REVERT: D 1281 ASN cc_start: 0.9219 (t0) cc_final: 0.8813 (t0) REVERT: D 1317 LYS cc_start: 0.9259 (ttmm) cc_final: 0.8924 (ttmt) REVERT: E 668 GLN cc_start: 0.9086 (tt0) cc_final: 0.8043 (tm-30) REVERT: E 690 MET cc_start: 0.8845 (tpp) cc_final: 0.8392 (mmm) REVERT: E 693 GLN cc_start: 0.9372 (tp40) cc_final: 0.8894 (tp40) REVERT: E 694 GLU cc_start: 0.9039 (tp30) cc_final: 0.8811 (tp30) REVERT: E 733 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7663 (pt0) REVERT: F 231 LYS cc_start: 0.8982 (tttt) cc_final: 0.8648 (ttmt) REVERT: F 237 LEU cc_start: 0.9385 (tp) cc_final: 0.9177 (tt) REVERT: F 249 LEU cc_start: 0.9343 (mt) cc_final: 0.9112 (mm) REVERT: F 274 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 1026 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8161 (mp10) REVERT: G 1077 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9081 (mmmt) REVERT: G 1084 ARG cc_start: 0.8965 (tpt170) cc_final: 0.8279 (tpp80) REVERT: G 1088 LEU cc_start: 0.9250 (mm) cc_final: 0.8897 (mm) REVERT: H 1482 LYS cc_start: 0.9258 (mttt) cc_final: 0.8864 (mmtt) REVERT: H 1490 GLU cc_start: 0.9055 (mp0) cc_final: 0.8808 (mp0) outliers start: 42 outliers final: 34 residues processed: 302 average time/residue: 0.2711 time to fit residues: 111.2060 Evaluate side-chains 308 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 496 SER 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 882 THR 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 1263 VAL Chi-restraints excluded: chain D residue 1277 LEU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1298 LEU Chi-restraints excluded: chain E residue 658 THR 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 E residue 726 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1020 SER Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 0.0070 chunk 62 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- 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 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3839 r_free = 0.3839 target = 0.102874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073077 restraints weight = 35256.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075462 restraints weight = 17404.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077062 restraints weight = 11686.526| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12230 Z= 0.166 Angle : 0.620 8.650 17678 Z= 0.361 Chirality : 0.035 0.206 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.075 173.911 3803 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.83 % Allowed : 34.30 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.31), residues: 730 helix: 1.85 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.47 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.015 0.001 PHE B 61 TYR 0.022 0.002 TYR D1318 ARG 0.006 0.001 ARG E 716 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 746) hydrogen bonds : angle 3.08421 ( 1879) covalent geometry : bond 0.00369 (12230) covalent geometry : angle 0.62026 (17678) *********************** 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 325 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7966 (pp20) cc_final: 0.7308 (pp20) REVERT: A 460 LEU cc_start: 0.8393 (mm) cc_final: 0.7647 (mt) REVERT: A 468 GLN cc_start: 0.9019 (tt0) cc_final: 0.8784 (tm-30) REVERT: A 473 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 485 GLN cc_start: 0.8644 (mt0) cc_final: 0.8319 (mt0) REVERT: A 494 GLU cc_start: 0.8739 (tp30) cc_final: 0.8483 (tp30) REVERT: B 35 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8447 (ttm110) REVERT: B 58 LEU cc_start: 0.9215 (tt) cc_final: 0.8986 (tt) REVERT: B 88 TYR cc_start: 0.8201 (m-10) cc_final: 0.7865 (m-80) REVERT: B 92 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8501 (ttt90) REVERT: C 821 GLN cc_start: 0.9099 (mp10) cc_final: 0.8766 (mp10) REVERT: C 822 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8606 (ttp80) REVERT: C 826 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8238 (mm-40) REVERT: C 853 TYR cc_start: 0.8559 (t80) cc_final: 0.8194 (t80) REVERT: C 867 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8734 (tm-30) REVERT: C 875 ASP cc_start: 0.8852 (m-30) cc_final: 0.8336 (p0) REVERT: C 879 LYS cc_start: 0.8977 (mttt) cc_final: 0.8374 (mtmt) REVERT: C 887 GLN cc_start: 0.9178 (tp40) cc_final: 0.8893 (tp-100) REVERT: C 901 LYS cc_start: 0.8644 (pttp) cc_final: 0.8252 (tptp) REVERT: C 912 HIS cc_start: 0.8323 (t70) cc_final: 0.7784 (t-90) REVERT: D 1268 GLU cc_start: 0.9069 (tp30) cc_final: 0.8569 (tp30) REVERT: D 1279 HIS cc_start: 0.8842 (t-90) cc_final: 0.8489 (t70) REVERT: D 1281 ASN cc_start: 0.9168 (t0) cc_final: 0.8770 (t0) REVERT: D 1317 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8896 (ttmt) REVERT: E 653 ARG cc_start: 0.8802 (tpt170) cc_final: 0.8518 (tpt170) REVERT: E 693 GLN cc_start: 0.9317 (tp40) cc_final: 0.8875 (tp40) REVERT: E 720 MET cc_start: 0.8714 (mmm) cc_final: 0.8326 (mmm) REVERT: E 733 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7553 (pt0) REVERT: F 231 LYS cc_start: 0.8990 (tttt) cc_final: 0.8689 (ttmt) REVERT: F 237 LEU cc_start: 0.9295 (tp) cc_final: 0.9095 (tt) REVERT: F 274 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8508 (tm-30) REVERT: F 290 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8855 (mt) REVERT: G 1026 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8156 (mp10) REVERT: G 1077 LYS cc_start: 0.9360 (mmmt) cc_final: 0.9097 (mmmt) REVERT: G 1079 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8696 (ptmm) REVERT: G 1084 ARG cc_start: 0.8946 (tpt170) cc_final: 0.8230 (tpp80) REVERT: G 1088 LEU cc_start: 0.9243 (mm) cc_final: 0.8913 (mm) REVERT: H 1432 GLU cc_start: 0.8016 (tp30) cc_final: 0.7456 (tp30) REVERT: H 1482 LYS cc_start: 0.9228 (mttt) cc_final: 0.8835 (mmtt) REVERT: H 1490 GLU cc_start: 0.9056 (mp0) cc_final: 0.8846 (mp0) outliers start: 36 outliers final: 27 residues processed: 302 average time/residue: 0.2771 time to fit residues: 113.7798 Evaluate side-chains 304 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 496 SER 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 C residue 882 THR 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 1273 GLU Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 658 THR 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 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1020 SER Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1066 LEU Chi-restraints excluded: chain H residue 1509 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073590 restraints weight = 33617.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.075818 restraints weight = 16893.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.077344 restraints weight = 11408.643| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12230 Z= 0.158 Angle : 0.614 8.437 17678 Z= 0.357 Chirality : 0.035 0.257 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.017 173.930 3803 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.69 % Allowed : 35.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 730 helix: 1.90 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.37 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 713 PHE 0.018 0.002 PHE A 467 TYR 0.020 0.002 TYR D1318 ARG 0.004 0.001 ARG C 831 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 746) hydrogen bonds : angle 3.05567 ( 1879) covalent geometry : bond 0.00351 (12230) covalent geometry : angle 0.61359 (17678) *********************** 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 316 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 1.050 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: 0.7992 (pp20) cc_final: 0.7238 (pm20) REVERT: A 473 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 476 GLN cc_start: 0.8649 (pp30) cc_final: 0.8390 (pp30) REVERT: A 494 GLU cc_start: 0.8704 (tp30) cc_final: 0.8477 (tp30) REVERT: A 507 THR cc_start: 0.9262 (t) cc_final: 0.9032 (t) REVERT: B 35 ARG cc_start: 0.9045 (ttm-80) cc_final: 0.8487 (ttm110) REVERT: B 58 LEU cc_start: 0.9151 (tt) cc_final: 0.8886 (tt) REVERT: B 88 TYR cc_start: 0.8196 (m-10) cc_final: 0.7860 (m-80) REVERT: B 92 ARG cc_start: 0.8906 (tmm-80) cc_final: 0.8298 (tmm-80) REVERT: C 821 GLN cc_start: 0.9092 (mp10) cc_final: 0.8762 (mp10) REVERT: C 822 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8686 (ttp80) REVERT: C 853 TYR cc_start: 0.8468 (t80) cc_final: 0.8121 (t80) REVERT: C 867 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8729 (tm-30) REVERT: C 875 ASP cc_start: 0.8862 (m-30) cc_final: 0.8297 (p0) REVERT: C 879 LYS cc_start: 0.9023 (mttt) cc_final: 0.8580 (mtmt) REVERT: C 887 GLN cc_start: 0.9161 (tp40) cc_final: 0.8870 (tp-100) REVERT: C 901 LYS cc_start: 0.8505 (pttp) cc_final: 0.7982 (tptp) REVERT: C 912 HIS cc_start: 0.8292 (t70) cc_final: 0.7909 (t70) REVERT: D 1268 GLU cc_start: 0.9020 (tp30) cc_final: 0.8491 (tp30) REVERT: D 1279 HIS cc_start: 0.8827 (t-90) cc_final: 0.8484 (t70) REVERT: D 1281 ASN cc_start: 0.9076 (t0) cc_final: 0.8730 (t0) REVERT: D 1317 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8941 (ttmt) REVERT: E 653 ARG cc_start: 0.8797 (tpt170) cc_final: 0.8512 (tpt170) REVERT: E 668 GLN cc_start: 0.9046 (tt0) cc_final: 0.8017 (tm-30) REVERT: E 685 GLN cc_start: 0.8237 (mt0) cc_final: 0.7939 (mt0) REVERT: E 693 GLN cc_start: 0.9233 (tp40) cc_final: 0.8784 (tp40) REVERT: E 720 MET cc_start: 0.8569 (mmm) cc_final: 0.8290 (mmm) REVERT: F 231 LYS cc_start: 0.8984 (tttt) cc_final: 0.8750 (ttmt) REVERT: F 274 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8414 (tm-30) REVERT: G 1026 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8130 (mp10) REVERT: G 1077 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9095 (mmmt) REVERT: G 1084 ARG cc_start: 0.8940 (tpt170) cc_final: 0.8202 (tpp80) REVERT: G 1088 LEU cc_start: 0.9160 (mm) cc_final: 0.8853 (mm) REVERT: H 1482 LYS cc_start: 0.9206 (mttt) cc_final: 0.8834 (mmtt) outliers start: 29 outliers final: 24 residues processed: 300 average time/residue: 0.2702 time to fit residues: 110.8077 Evaluate side-chains 298 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 496 SER 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 882 THR 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 1277 LEU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1298 LEU Chi-restraints excluded: chain E residue 658 THR 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 229 ILE 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 H residue 1509 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.068939 restraints weight = 33232.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071015 restraints weight = 17005.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072408 restraints weight = 11624.114| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12230 Z= 0.285 Angle : 0.692 9.574 17678 Z= 0.396 Chirality : 0.038 0.200 2019 Planarity : 0.005 0.068 1290 Dihedral : 31.247 173.654 3803 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.50 % Allowed : 36.08 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.31), residues: 730 helix: 1.77 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.51 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 713 PHE 0.028 0.003 PHE B 61 TYR 0.029 0.003 TYR D1318 ARG 0.007 0.001 ARG D1296 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 746) hydrogen bonds : angle 3.45329 ( 1879) covalent geometry : bond 0.00642 (12230) covalent geometry : angle 0.69164 (17678) ********************** 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 298 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8169 (pp20) cc_final: 0.7828 (pp20) REVERT: A 473 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 528 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8099 (ttp80) REVERT: B 35 ARG cc_start: 0.9088 (ttm-80) cc_final: 0.8398 (ttm110) REVERT: B 92 ARG cc_start: 0.8967 (tmm-80) cc_final: 0.8619 (ttt90) REVERT: C 821 GLN cc_start: 0.9099 (mp10) cc_final: 0.8772 (mp10) REVERT: C 822 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8802 (ttp80) REVERT: C 853 TYR cc_start: 0.8574 (t80) cc_final: 0.8193 (t80) REVERT: C 867 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8781 (tm-30) REVERT: C 875 ASP cc_start: 0.8856 (m-30) cc_final: 0.8343 (p0) REVERT: C 879 LYS cc_start: 0.8994 (mttt) cc_final: 0.8407 (mtmt) REVERT: C 887 GLN cc_start: 0.9192 (tp40) cc_final: 0.8908 (tp-100) REVERT: C 901 LYS cc_start: 0.8587 (pttp) cc_final: 0.7870 (tptp) REVERT: C 912 HIS cc_start: 0.8342 (t70) cc_final: 0.7916 (t70) REVERT: D 1268 GLU cc_start: 0.9090 (tp30) cc_final: 0.8603 (tp30) REVERT: D 1281 ASN cc_start: 0.9247 (t0) cc_final: 0.8849 (t0) REVERT: D 1317 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8921 (ttmt) REVERT: E 668 GLN cc_start: 0.9107 (tt0) cc_final: 0.7995 (tm-30) REVERT: E 685 GLN cc_start: 0.8581 (mt0) cc_final: 0.8138 (mt0) REVERT: E 693 GLN cc_start: 0.9288 (tp40) cc_final: 0.8814 (tp40) REVERT: E 733 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7502 (pt0) REVERT: F 231 LYS cc_start: 0.9046 (tttt) cc_final: 0.8686 (ttmt) REVERT: F 274 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8507 (tm-30) REVERT: G 1026 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8158 (mp10) REVERT: G 1077 LYS cc_start: 0.9334 (mmmt) cc_final: 0.9065 (mmmt) REVERT: G 1084 ARG cc_start: 0.8983 (tpt170) cc_final: 0.8288 (tpp80) REVERT: G 1088 LEU cc_start: 0.9298 (mm) cc_final: 0.8957 (mm) REVERT: H 1482 LYS cc_start: 0.9213 (mttt) cc_final: 0.8786 (mmtt) outliers start: 34 outliers final: 31 residues processed: 281 average time/residue: 0.2611 time to fit residues: 99.3285 Evaluate side-chains 286 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 496 SER 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 62 LEU Chi-restraints excluded: chain C residue 882 THR 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 1263 VAL Chi-restraints excluded: chain D residue 1273 GLU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1298 LEU Chi-restraints excluded: chain E residue 658 THR 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 707 THR 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 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1020 SER Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR 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 89 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 676 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.100760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073600 restraints weight = 33252.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075864 restraints weight = 16426.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.077385 restraints weight = 10939.352| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12230 Z= 0.162 Angle : 0.647 8.433 17678 Z= 0.371 Chirality : 0.035 0.196 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.041 174.074 3803 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.05 % Allowed : 36.25 % Favored : 59.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.31), residues: 730 helix: 1.76 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.44 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D1306 PHE 0.028 0.002 PHE A 467 TYR 0.024 0.002 TYR B 88 ARG 0.005 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 746) hydrogen bonds : angle 3.17820 ( 1879) covalent geometry : bond 0.00360 (12230) covalent geometry : angle 0.64673 (17678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.77 seconds wall clock time: 70 minutes 29.97 seconds (4229.97 seconds total)