Starting phenix.real_space_refine on Wed May 14 01:47:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m1x_23626/05_2025/7m1x_23626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1x_23626/05_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_23626/05_2025/7m1x_23626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1x_23626/05_2025/7m1x_23626.map" model { file = "/net/cci-nas-00/data/ceres_data/7m1x_23626/05_2025/7m1x_23626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1x_23626/05_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-5687/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: 7.04, per 1000 atoms: 0.61 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: 2.90 Conformation dependent library (CDL) restraints added in 935.9 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 74.3% alpha, 1.9% beta 135 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 5.59 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: 8.25 Time building geometry restraints manager: 3.41 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: 0.430 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.270 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- 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 : 0.885 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: 0.2938 time to fit residues: 136.7421 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 : 0.904 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.098609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071009 restraints weight = 33240.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073231 restraints weight = 16345.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074708 restraints weight = 11002.527| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.8976 (tt0) cc_final: 0.8368 (tm-30) REVERT: A 473 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 485 GLN cc_start: 0.8725 (mt0) cc_final: 0.8320 (mt0) REVERT: A 520 MET cc_start: 0.8055 (mtt) cc_final: 0.7602 (mtp) REVERT: B 52 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8342 (tp30) REVERT: B 81 VAL cc_start: 0.9352 (t) cc_final: 0.8989 (p) REVERT: B 92 ARG cc_start: 0.8748 (tmm-80) cc_final: 0.8008 (tmm-80) REVERT: C 822 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8821 (ttt-90) REVERT: C 837 LYS cc_start: 0.8879 (tppt) cc_final: 0.8634 (ttpp) REVERT: C 853 TYR cc_start: 0.8747 (t80) cc_final: 0.8175 (t80) REVERT: C 867 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 875 ASP cc_start: 0.8831 (m-30) cc_final: 0.8298 (p0) REVERT: C 884 ARG cc_start: 0.8930 (tpt170) cc_final: 0.8670 (tpt170) REVERT: C 887 GLN cc_start: 0.9188 (tp40) cc_final: 0.8871 (tp-100) REVERT: C 901 LYS cc_start: 0.8872 (pttp) cc_final: 0.8275 (tptp) REVERT: C 912 HIS cc_start: 0.8280 (t70) cc_final: 0.7715 (t-90) REVERT: D 1243 LYS cc_start: 0.9243 (mmtt) cc_final: 0.8342 (mmmt) REVERT: D 1268 GLU cc_start: 0.8929 (tp30) cc_final: 0.8712 (tp30) REVERT: D 1279 HIS cc_start: 0.8661 (t-90) cc_final: 0.8015 (t70) REVERT: D 1281 ASN cc_start: 0.9308 (t0) cc_final: 0.8901 (t0) REVERT: D 1317 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8977 (ttmt) REVERT: E 705 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 720 MET cc_start: 0.8785 (tpp) cc_final: 0.8349 (mmm) REVERT: E 725 GLN cc_start: 0.9173 (mt0) cc_final: 0.8897 (mt0) REVERT: F 231 LYS cc_start: 0.8839 (tttt) cc_final: 0.8623 (ttmt) REVERT: F 244 LYS cc_start: 0.9086 (tttt) cc_final: 0.8735 (tttt) REVERT: F 249 LEU cc_start: 0.9220 (mt) cc_final: 0.8804 (mt) REVERT: F 252 GLU cc_start: 0.8724 (mp0) cc_final: 0.8409 (pm20) REVERT: F 274 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8726 (tm-30) REVERT: F 284 MET cc_start: 0.8904 (tpp) cc_final: 0.8319 (mmm) REVERT: F 291 LYS cc_start: 0.9025 (tttp) cc_final: 0.8624 (ttpt) REVERT: G 1059 GLU cc_start: 0.8652 (tt0) cc_final: 0.8404 (tt0) REVERT: G 1084 ARG cc_start: 0.8917 (tpt170) cc_final: 0.8443 (tpp80) REVERT: G 1088 LEU cc_start: 0.9290 (mm) cc_final: 0.8951 (mm) REVERT: H 1433 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8891 (m) REVERT: H 1461 SER cc_start: 0.9478 (t) cc_final: 0.9253 (t) REVERT: H 1465 ASP cc_start: 0.9205 (t70) cc_final: 0.8912 (t0) REVERT: H 1468 GLU cc_start: 0.8571 (tp30) cc_final: 0.8322 (tt0) REVERT: H 1469 ARG cc_start: 0.9243 (ttm170) cc_final: 0.9020 (mtm180) REVERT: H 1486 ILE cc_start: 0.8972 (mt) cc_final: 0.8620 (mt) outliers start: 25 outliers final: 15 residues processed: 330 average time/residue: 0.2881 time to fit residues: 125.7988 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 : 0.911 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 GLN E 668 GLN G1033 HIS ** G1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.097851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069813 restraints weight = 32277.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.071996 restraints weight = 15675.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.073429 restraints weight = 10500.282| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12230 Z= 0.213 Angle : 0.619 7.814 17678 Z= 0.364 Chirality : 0.035 0.165 2019 Planarity : 0.004 0.053 1290 Dihedral : 31.352 174.010 3805 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.34 % Allowed : 28.48 % Favored : 66.18 % 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: 1.00 (0.30), residues: 730 helix: 1.84 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 275 PHE 0.011 0.002 PHE E 667 TYR 0.023 0.002 TYR D1318 ARG 0.006 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 746) hydrogen bonds : angle 3.15639 ( 1879) covalent geometry : bond 0.00472 (12230) covalent geometry : angle 0.61904 (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 328 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8013 (pp20) cc_final: 0.7708 (pp20) REVERT: A 468 GLN cc_start: 0.9079 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 520 MET cc_start: 0.8289 (mtt) cc_final: 0.7753 (mtp) REVERT: B 92 ARG cc_start: 0.8837 (tmm-80) cc_final: 0.8364 (tmm-80) REVERT: C 821 GLN cc_start: 0.9156 (mp10) cc_final: 0.8868 (mp10) REVERT: C 822 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8856 (ttt-90) REVERT: C 853 TYR cc_start: 0.8801 (t80) cc_final: 0.8124 (t80) REVERT: C 867 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 884 ARG cc_start: 0.8868 (tpt170) cc_final: 0.8553 (tpt170) REVERT: C 887 GLN cc_start: 0.9171 (tp40) cc_final: 0.8878 (tp-100) REVERT: C 901 LYS cc_start: 0.8954 (pttp) cc_final: 0.8431 (tptp) REVERT: C 912 HIS cc_start: 0.8353 (t70) cc_final: 0.7795 (t-90) REVERT: D 1268 GLU cc_start: 0.9042 (tp30) cc_final: 0.8804 (tp30) REVERT: D 1281 ASN cc_start: 0.9319 (t0) cc_final: 0.8911 (t0) REVERT: D 1317 LYS cc_start: 0.9345 (ttmm) cc_final: 0.8999 (ttmt) REVERT: E 693 GLN cc_start: 0.9317 (tp40) cc_final: 0.8960 (tp40) REVERT: E 694 GLU cc_start: 0.9004 (tp30) cc_final: 0.8567 (tp30) REVERT: E 697 GLU cc_start: 0.7863 (pp20) cc_final: 0.7441 (pp20) REVERT: E 705 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8452 (tm-30) REVERT: E 708 ASN cc_start: 0.9401 (t0) cc_final: 0.9062 (t0) REVERT: E 720 MET cc_start: 0.8817 (tpp) cc_final: 0.8522 (mmm) REVERT: F 231 LYS cc_start: 0.9048 (tttt) cc_final: 0.8830 (ttmt) REVERT: F 244 LYS cc_start: 0.9136 (tttt) cc_final: 0.8465 (tttt) REVERT: F 249 LEU cc_start: 0.9243 (mt) cc_final: 0.8966 (mt) REVERT: F 252 GLU cc_start: 0.8786 (mp0) cc_final: 0.8536 (pm20) REVERT: F 274 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8636 (tm-30) REVERT: F 284 MET cc_start: 0.8882 (tpp) cc_final: 0.8672 (tpp) REVERT: F 291 LYS cc_start: 0.9110 (tttp) cc_final: 0.8910 (tttt) REVERT: G 1021 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: G 1045 ARG cc_start: 0.9350 (ptm160) cc_final: 0.9026 (ptm160) REVERT: G 1079 LYS cc_start: 0.9288 (ttmm) cc_final: 0.9030 (ttpt) REVERT: G 1084 ARG cc_start: 0.8937 (tpt170) cc_final: 0.8450 (tpp80) REVERT: G 1087 GLN cc_start: 0.9059 (tp40) cc_final: 0.8858 (tp40) REVERT: G 1088 LEU cc_start: 0.9302 (mm) cc_final: 0.8987 (mm) REVERT: H 1468 GLU cc_start: 0.8604 (tp30) cc_final: 0.8383 (tt0) REVERT: H 1486 ILE cc_start: 0.9038 (mt) cc_final: 0.8726 (mt) outliers start: 33 outliers final: 27 residues processed: 309 average time/residue: 0.2683 time to fit residues: 111.9609 Evaluate side-chains 299 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 C residue 862 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1017 VAL 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 G residue 1065 VAL 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: 0.2980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 ** G1087 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 = 0.3745 r_free = 0.3745 target = 0.097839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070537 restraints weight = 33306.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072710 restraints weight = 16400.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074145 restraints weight = 11002.293| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12230 Z= 0.171 Angle : 0.600 8.191 17678 Z= 0.355 Chirality : 0.035 0.167 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.180 174.057 3803 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.50 % Allowed : 32.20 % Favored : 62.30 % 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 (0.31), residues: 730 helix: 2.01 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -2.60 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 275 PHE 0.014 0.001 PHE B 61 TYR 0.026 0.002 TYR H1480 ARG 0.005 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 746) hydrogen bonds : angle 3.00672 ( 1879) covalent geometry : bond 0.00378 (12230) covalent geometry : angle 0.59991 (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 327 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7927 (pp20) cc_final: 0.7605 (pp20) REVERT: A 468 GLN cc_start: 0.9051 (tt0) cc_final: 0.8460 (tm-30) REVERT: A 485 GLN cc_start: 0.8737 (mt0) cc_final: 0.8456 (mt0) REVERT: A 520 MET cc_start: 0.8194 (mtt) cc_final: 0.7606 (mtp) REVERT: B 35 ARG cc_start: 0.9156 (ttm-80) cc_final: 0.8447 (ttm110) REVERT: B 92 ARG cc_start: 0.8833 (tmm-80) cc_final: 0.8329 (tmm-80) REVERT: C 821 GLN cc_start: 0.9138 (mp10) cc_final: 0.8823 (mp10) REVERT: C 822 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8764 (ttt-90) REVERT: C 826 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8193 (mm-40) REVERT: C 853 TYR cc_start: 0.8679 (t80) cc_final: 0.7990 (t80) REVERT: C 867 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8773 (tm-30) REVERT: C 875 ASP cc_start: 0.8862 (m-30) cc_final: 0.8350 (p0) REVERT: C 887 GLN cc_start: 0.9132 (tp40) cc_final: 0.8858 (tp-100) REVERT: C 901 LYS cc_start: 0.8810 (pttp) cc_final: 0.8354 (tptp) REVERT: C 912 HIS cc_start: 0.8361 (t70) cc_final: 0.7885 (t-90) REVERT: D 1268 GLU cc_start: 0.9077 (tp30) cc_final: 0.8743 (tp30) REVERT: D 1281 ASN cc_start: 0.9268 (t0) cc_final: 0.8881 (t0) REVERT: D 1317 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8956 (ttmt) REVERT: E 668 GLN cc_start: 0.9067 (tt0) cc_final: 0.8124 (tm-30) REVERT: E 690 MET cc_start: 0.8921 (mmm) cc_final: 0.8674 (tpp) REVERT: E 693 GLN cc_start: 0.9348 (tp40) cc_final: 0.8882 (tp40) REVERT: E 705 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 720 MET cc_start: 0.8892 (tpp) cc_final: 0.8561 (mmm) REVERT: E 733 GLU cc_start: 0.8173 (pt0) cc_final: 0.7601 (pt0) REVERT: F 231 LYS cc_start: 0.9022 (tttt) cc_final: 0.8791 (ttmt) REVERT: F 274 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8645 (tm-30) REVERT: F 279 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8272 (mtmt) REVERT: F 291 LYS cc_start: 0.9070 (tttp) cc_final: 0.8863 (tttt) REVERT: G 1045 ARG cc_start: 0.9397 (ptm160) cc_final: 0.8994 (ptm160) REVERT: G 1079 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9054 (ttpt) REVERT: G 1084 ARG cc_start: 0.8935 (tpt170) cc_final: 0.8420 (tpp80) REVERT: G 1088 LEU cc_start: 0.9250 (mm) cc_final: 0.8892 (mm) REVERT: H 1468 GLU cc_start: 0.8694 (tp30) cc_final: 0.8441 (tt0) REVERT: H 1482 LYS cc_start: 0.9226 (mttt) cc_final: 0.8843 (mmtt) REVERT: H 1490 GLU cc_start: 0.9145 (mp0) cc_final: 0.8905 (mp0) outliers start: 34 outliers final: 23 residues processed: 309 average time/residue: 0.2723 time to fit residues: 113.3846 Evaluate side-chains 298 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 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 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1073 SER 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: 4.9990 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.099994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072808 restraints weight = 33095.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075058 restraints weight = 16292.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076536 restraints weight = 10906.730| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12230 Z= 0.160 Angle : 0.594 7.097 17678 Z= 0.349 Chirality : 0.034 0.177 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.077 174.052 3803 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.18 % Allowed : 32.52 % Favored : 62.30 % 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: 1.31 (0.31), residues: 730 helix: 2.05 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.59 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.027 0.002 PHE A 467 TYR 0.023 0.002 TYR D1318 ARG 0.006 0.000 ARG G1034 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 746) hydrogen bonds : angle 2.94173 ( 1879) covalent geometry : bond 0.00351 (12230) covalent geometry : angle 0.59434 (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 327 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7974 (pp20) cc_final: 0.7598 (pp20) REVERT: A 460 LEU cc_start: 0.8450 (mm) cc_final: 0.7944 (mt) REVERT: B 35 ARG cc_start: 0.9102 (ttm-80) cc_final: 0.8477 (ttm110) REVERT: B 58 LEU cc_start: 0.9253 (tt) cc_final: 0.9029 (tt) REVERT: B 88 TYR cc_start: 0.7881 (m-80) cc_final: 0.7523 (m-80) REVERT: B 92 ARG cc_start: 0.8865 (tmm-80) cc_final: 0.8370 (tmm-80) REVERT: C 821 GLN cc_start: 0.9086 (mp10) cc_final: 0.8782 (mp10) REVERT: C 822 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8689 (ttt-90) REVERT: C 853 TYR cc_start: 0.8554 (t80) cc_final: 0.8052 (t80) REVERT: C 867 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8741 (tm-30) REVERT: C 875 ASP cc_start: 0.8832 (m-30) cc_final: 0.8334 (p0) REVERT: C 887 GLN cc_start: 0.9163 (tp40) cc_final: 0.8884 (tp-100) REVERT: C 901 LYS cc_start: 0.8699 (pttp) cc_final: 0.8224 (tptp) REVERT: C 912 HIS cc_start: 0.8302 (t70) cc_final: 0.7727 (t-90) REVERT: D 1268 GLU cc_start: 0.9031 (tp30) cc_final: 0.8564 (tp30) REVERT: D 1279 HIS cc_start: 0.8920 (t-90) cc_final: 0.8489 (t-170) REVERT: D 1281 ASN cc_start: 0.9193 (t0) cc_final: 0.8772 (t0) REVERT: D 1317 LYS cc_start: 0.9273 (ttmm) cc_final: 0.8936 (ttmt) REVERT: E 693 GLN cc_start: 0.9321 (tp40) cc_final: 0.8761 (tp40) REVERT: E 705 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8500 (tm-30) REVERT: E 733 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: F 231 LYS cc_start: 0.9091 (tttt) cc_final: 0.8860 (ttmt) REVERT: F 244 LYS cc_start: 0.9039 (tttt) cc_final: 0.8347 (tttt) REVERT: F 247 SER cc_start: 0.8575 (p) cc_final: 0.8319 (t) REVERT: F 250 ILE cc_start: 0.9660 (tp) cc_final: 0.9457 (mm) REVERT: F 274 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8576 (tm-30) REVERT: F 279 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8258 (mtmt) REVERT: G 1026 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8022 (mp10) REVERT: G 1077 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8968 (mmmt) REVERT: G 1084 ARG cc_start: 0.8917 (tpt170) cc_final: 0.8193 (tpp80) REVERT: G 1088 LEU cc_start: 0.9213 (mm) cc_final: 0.8911 (mm) REVERT: H 1468 GLU cc_start: 0.8677 (tp30) cc_final: 0.8444 (tt0) REVERT: H 1482 LYS cc_start: 0.9254 (mttt) cc_final: 0.8887 (mmtt) outliers start: 32 outliers final: 27 residues processed: 309 average time/residue: 0.2737 time to fit residues: 115.3869 Evaluate side-chains 312 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 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 1249 THR Chi-restraints excluded: chain D residue 1275 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 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1073 SER Chi-restraints excluded: chain H residue 1488 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: 0.7980 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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** ** G1087 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 = 0.3813 r_free = 0.3813 target = 0.101140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071668 restraints weight = 35200.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.074023 restraints weight = 17396.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075615 restraints weight = 11638.609| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12230 Z= 0.203 Angle : 0.622 13.163 17678 Z= 0.361 Chirality : 0.035 0.188 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.127 173.900 3803 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.44 % Allowed : 31.23 % Favored : 61.33 % 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: 1.17 (0.31), residues: 730 helix: 1.93 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.012 0.002 PHE D1267 TYR 0.024 0.002 TYR D1318 ARG 0.004 0.000 ARG G1034 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 746) hydrogen bonds : angle 3.06926 ( 1879) covalent geometry : bond 0.00455 (12230) covalent geometry : angle 0.62228 (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 328 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.925 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: 0.8078 (pp20) cc_final: 0.7413 (pp20) REVERT: A 460 LEU cc_start: 0.8434 (mm) cc_final: 0.7801 (mt) REVERT: A 468 GLN cc_start: 0.9091 (tt0) cc_final: 0.8501 (tm-30) REVERT: A 528 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: B 35 ARG cc_start: 0.9089 (ttm-80) cc_final: 0.8446 (ttm110) REVERT: B 88 TYR cc_start: 0.8033 (m-80) cc_final: 0.7733 (m-80) REVERT: B 92 ARG cc_start: 0.8912 (tmm-80) cc_final: 0.8271 (tmm-80) REVERT: C 821 GLN cc_start: 0.9099 (mp10) cc_final: 0.8792 (mp10) REVERT: C 822 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8668 (ttp80) REVERT: C 853 TYR cc_start: 0.8608 (t80) cc_final: 0.8152 (t80) REVERT: C 867 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 875 ASP cc_start: 0.8851 (m-30) cc_final: 0.8335 (p0) REVERT: C 887 GLN cc_start: 0.9189 (tp40) cc_final: 0.8900 (tp-100) REVERT: C 901 LYS cc_start: 0.8713 (pttp) cc_final: 0.8291 (tptp) REVERT: C 912 HIS cc_start: 0.8372 (t70) cc_final: 0.7779 (t-90) REVERT: D 1268 GLU cc_start: 0.9090 (tp30) cc_final: 0.8651 (tp30) REVERT: D 1279 HIS cc_start: 0.8860 (t-90) cc_final: 0.8567 (t70) REVERT: D 1281 ASN cc_start: 0.9175 (t0) cc_final: 0.8766 (t0) REVERT: D 1317 LYS cc_start: 0.9255 (ttmm) cc_final: 0.8933 (ttmt) REVERT: E 668 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: E 690 MET cc_start: 0.8928 (mmm) cc_final: 0.8641 (tpp) REVERT: E 693 GLN cc_start: 0.9369 (tp40) cc_final: 0.8917 (tp40) REVERT: E 694 GLU cc_start: 0.9022 (tp30) cc_final: 0.8782 (tp30) REVERT: E 705 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 708 ASN cc_start: 0.9267 (t0) cc_final: 0.9025 (t0) REVERT: E 720 MET cc_start: 0.8790 (mmm) cc_final: 0.8553 (mmt) REVERT: E 733 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: F 231 LYS cc_start: 0.9150 (tttt) cc_final: 0.8926 (ttmt) REVERT: F 244 LYS cc_start: 0.9014 (tttt) cc_final: 0.8351 (tttt) REVERT: F 274 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8589 (tm-30) REVERT: G 1026 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8099 (mp10) REVERT: G 1084 ARG cc_start: 0.8967 (tpt170) cc_final: 0.8247 (tpp80) REVERT: G 1088 LEU cc_start: 0.9246 (mm) cc_final: 0.8938 (mm) REVERT: H 1468 GLU cc_start: 0.8717 (tp30) cc_final: 0.8492 (tt0) REVERT: H 1482 LYS cc_start: 0.9244 (mttt) cc_final: 0.8863 (mmtt) REVERT: H 1490 GLU cc_start: 0.9053 (mp0) cc_final: 0.8778 (pm20) outliers start: 46 outliers final: 36 residues processed: 301 average time/residue: 0.2683 time to fit residues: 109.6670 Evaluate side-chains 307 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1273 GLU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 668 GLN 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 733 GLU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1066 LEU Chi-restraints excluded: chain G residue 1073 SER Chi-restraints excluded: chain H residue 1433 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: 4.9990 chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** ** G1087 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 = 0.3784 r_free = 0.3784 target = 0.096876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069917 restraints weight = 33831.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072056 restraints weight = 16656.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073530 restraints weight = 11137.859| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12230 Z= 0.246 Angle : 0.655 10.750 17678 Z= 0.379 Chirality : 0.037 0.202 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.203 173.796 3803 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 7.77 % Allowed : 33.66 % Favored : 58.58 % 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: 1.09 (0.31), residues: 730 helix: 1.86 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.68 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 275 PHE 0.016 0.002 PHE D1267 TYR 0.026 0.002 TYR D1318 ARG 0.006 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 746) hydrogen bonds : angle 3.29099 ( 1879) covalent geometry : bond 0.00551 (12230) covalent geometry : angle 0.65451 (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 321 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.918 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: 0.7380 (pp20) REVERT: A 460 LEU cc_start: 0.8489 (mm) cc_final: 0.7678 (mt) REVERT: A 468 GLN cc_start: 0.9180 (tt0) cc_final: 0.8640 (tm-30) REVERT: A 473 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 35 ARG cc_start: 0.9099 (ttm-80) cc_final: 0.8399 (ttm110) REVERT: B 88 TYR cc_start: 0.8253 (m-80) cc_final: 0.8021 (m-80) REVERT: B 92 ARG cc_start: 0.8952 (tmm-80) cc_final: 0.8633 (ttt90) REVERT: B 97 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9208 (tp) REVERT: C 821 GLN cc_start: 0.9111 (mp10) cc_final: 0.8795 (mp10) REVERT: C 822 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8731 (ttp80) REVERT: C 853 TYR cc_start: 0.8616 (t80) cc_final: 0.8164 (t80) REVERT: C 867 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8784 (tm-30) REVERT: C 875 ASP cc_start: 0.8850 (m-30) cc_final: 0.8353 (p0) REVERT: C 887 GLN cc_start: 0.9221 (tp40) cc_final: 0.8923 (tp-100) REVERT: C 912 HIS cc_start: 0.8375 (t70) cc_final: 0.7786 (t-90) REVERT: D 1268 GLU cc_start: 0.9064 (tp30) cc_final: 0.8562 (tp30) REVERT: D 1279 HIS cc_start: 0.8835 (t-90) cc_final: 0.8474 (t70) REVERT: D 1281 ASN cc_start: 0.9261 (t0) cc_final: 0.8858 (t0) REVERT: D 1317 LYS cc_start: 0.9256 (ttmm) cc_final: 0.8934 (ttmt) REVERT: E 668 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: E 690 MET cc_start: 0.8986 (mmm) cc_final: 0.8705 (tpp) REVERT: E 693 GLN cc_start: 0.9333 (tp40) cc_final: 0.8831 (tp40) REVERT: E 704 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8622 (m-10) REVERT: E 708 ASN cc_start: 0.9295 (t0) cc_final: 0.8929 (t0) REVERT: E 733 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: F 231 LYS cc_start: 0.9136 (tttt) cc_final: 0.8821 (ttmt) REVERT: F 244 LYS cc_start: 0.9001 (tttt) cc_final: 0.8709 (tttt) REVERT: F 274 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8635 (tm-30) REVERT: G 1026 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8101 (mp10) REVERT: G 1079 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8641 (ptmm) REVERT: G 1084 ARG cc_start: 0.8977 (tpt170) cc_final: 0.8411 (tpp80) REVERT: G 1088 LEU cc_start: 0.9300 (mm) cc_final: 0.8942 (mm) REVERT: H 1482 LYS cc_start: 0.9228 (mttt) cc_final: 0.8810 (mmtt) outliers start: 48 outliers final: 40 residues processed: 295 average time/residue: 0.2623 time to fit residues: 105.1195 Evaluate side-chains 308 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1273 GLU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 668 GLN 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 704 PHE Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1020 SER Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1066 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1488 SER 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: 0.8980 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** G1087 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 = 0.3842 r_free = 0.3842 target = 0.100714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072771 restraints weight = 33760.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.074991 restraints weight = 16968.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.076503 restraints weight = 11465.416| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12230 Z= 0.157 Angle : 0.616 9.781 17678 Z= 0.359 Chirality : 0.035 0.269 2019 Planarity : 0.004 0.052 1290 Dihedral : 31.033 174.259 3803 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.53 % Allowed : 37.38 % Favored : 58.09 % 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: 1.17 (0.31), residues: 730 helix: 1.94 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.63 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 275 PHE 0.021 0.002 PHE A 467 TYR 0.021 0.002 TYR D1318 ARG 0.006 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 746) hydrogen bonds : angle 3.03017 ( 1879) covalent geometry : bond 0.00346 (12230) covalent geometry : angle 0.61608 (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 317 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 0.962 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: 0.7924 (pp20) cc_final: 0.7107 (pm20) REVERT: A 468 GLN cc_start: 0.9054 (tt0) cc_final: 0.8458 (tm-30) REVERT: A 507 THR cc_start: 0.9267 (t) cc_final: 0.9029 (t) REVERT: B 35 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8399 (ttm110) REVERT: B 58 LEU cc_start: 0.9149 (tt) cc_final: 0.8870 (tt) REVERT: B 88 TYR cc_start: 0.8236 (m-80) cc_final: 0.7988 (m-80) REVERT: B 92 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8512 (ttt90) REVERT: C 821 GLN cc_start: 0.9122 (mp10) cc_final: 0.8793 (mp10) REVERT: C 822 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8623 (ttt90) REVERT: C 853 TYR cc_start: 0.8495 (t80) cc_final: 0.8138 (t80) REVERT: C 867 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 875 ASP cc_start: 0.8835 (m-30) cc_final: 0.8348 (p0) REVERT: C 887 GLN cc_start: 0.9163 (tp40) cc_final: 0.8864 (tp-100) REVERT: C 901 LYS cc_start: 0.8531 (pttp) cc_final: 0.8049 (tptp) REVERT: C 912 HIS cc_start: 0.8373 (t70) cc_final: 0.7836 (t-90) REVERT: D 1268 GLU cc_start: 0.9023 (tp30) cc_final: 0.8520 (tp30) REVERT: D 1279 HIS cc_start: 0.8825 (t-90) cc_final: 0.8507 (t70) REVERT: D 1281 ASN cc_start: 0.9169 (t0) cc_final: 0.8785 (t0) REVERT: D 1306 HIS cc_start: 0.9041 (m170) cc_final: 0.8814 (m170) REVERT: D 1317 LYS cc_start: 0.9235 (ttmm) cc_final: 0.8901 (ttmt) REVERT: E 668 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: E 693 GLN cc_start: 0.9265 (tp40) cc_final: 0.8705 (tp40) REVERT: E 708 ASN cc_start: 0.9262 (t0) cc_final: 0.8872 (t0) REVERT: E 720 MET cc_start: 0.8833 (mmt) cc_final: 0.8483 (mmm) REVERT: E 733 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: F 231 LYS cc_start: 0.9094 (tttt) cc_final: 0.8628 (ttmt) REVERT: F 237 LEU cc_start: 0.9309 (tp) cc_final: 0.9064 (tt) REVERT: F 244 LYS cc_start: 0.9005 (tttt) cc_final: 0.8708 (tttt) REVERT: F 274 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8517 (tm-30) REVERT: G 1077 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8955 (mmmt) REVERT: G 1084 ARG cc_start: 0.8932 (tpt170) cc_final: 0.8182 (tpp80) REVERT: G 1088 LEU cc_start: 0.9229 (mm) cc_final: 0.8902 (mm) REVERT: H 1482 LYS cc_start: 0.9238 (mttt) cc_final: 0.8852 (mmtt) REVERT: H 1490 GLU cc_start: 0.9025 (pm20) cc_final: 0.8584 (pm20) outliers start: 28 outliers final: 22 residues processed: 300 average time/residue: 0.2668 time to fit residues: 108.8591 Evaluate side-chains 300 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1249 THR Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 668 GLN 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 E residue 733 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9037 > 50: distance: 33 - 34: 10.355 distance: 34 - 35: 40.378 distance: 34 - 37: 8.928 distance: 35 - 36: 21.220 distance: 35 - 44: 38.835 distance: 37 - 38: 40.192 distance: 38 - 39: 33.454 distance: 39 - 40: 15.296 distance: 40 - 41: 15.168 distance: 44 - 45: 28.322 distance: 45 - 46: 9.814 distance: 45 - 48: 58.896 distance: 46 - 47: 22.382 distance: 46 - 52: 18.001 distance: 47 - 68: 19.098 distance: 48 - 49: 34.875 distance: 49 - 50: 15.761 distance: 52 - 53: 12.415 distance: 53 - 54: 19.838 distance: 53 - 56: 25.553 distance: 54 - 55: 12.813 distance: 54 - 60: 10.189 distance: 56 - 57: 23.314 distance: 57 - 58: 8.770 distance: 60 - 61: 29.039 distance: 61 - 62: 11.405 distance: 61 - 64: 23.108 distance: 62 - 63: 11.893 distance: 62 - 68: 23.482 distance: 63 - 81: 61.608 distance: 64 - 65: 36.632 distance: 64 - 66: 13.872 distance: 65 - 67: 19.229 distance: 68 - 69: 41.013 distance: 69 - 72: 5.785 distance: 72 - 73: 35.373 distance: 73 - 74: 4.722 distance: 74 - 75: 34.198 distance: 74 - 76: 67.339 distance: 77 - 78: 41.142 distance: 78 - 79: 56.559 distance: 79 - 80: 14.928 distance: 79 - 81: 47.287 distance: 82 - 83: 27.908 distance: 82 - 85: 39.930 distance: 83 - 84: 4.387 distance: 83 - 89: 4.547 distance: 85 - 86: 40.769 distance: 85 - 87: 40.344 distance: 86 - 88: 38.794 distance: 89 - 90: 32.073 distance: 90 - 91: 35.755 distance: 90 - 93: 11.584 distance: 91 - 92: 34.392 distance: 91 - 96: 14.101 distance: 92 - 117: 34.800 distance: 93 - 94: 40.092 distance: 96 - 97: 4.360 distance: 97 - 98: 56.531 distance: 97 - 100: 41.563 distance: 98 - 99: 51.165 distance: 98 - 105: 28.355 distance: 99 - 125: 30.640 distance: 100 - 101: 11.620 distance: 101 - 102: 10.273 distance: 102 - 103: 8.743 distance: 103 - 104: 30.682