Starting phenix.real_space_refine on Thu Feb 15 06:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_23626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_23626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_23626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_23626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1x_23626/02_2024/7m1x_23626.pdb" } 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 Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 893": "OD1" <-> "OD2" Residue "D TYR 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1268": "OE1" <-> "OE2" Residue "D GLU 1302": "OE1" <-> "OE2" Residue "D TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 697": "OE1" <-> "OE2" Residue "E ASP 723": "OD1" <-> "OD2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1075": "OD1" <-> "OD2" Residue "H TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1468": "OE1" <-> "OE2" Residue "H GLU 1502": "OE1" <-> "OE2" Residue "H TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.12, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 5.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 74.3% alpha, 1.9% beta 135 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 4.85 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: 7.12 Time building geometry restraints manager: 6.22 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: 97.19 - 104.28: 1033 104.28 - 111.37: 6254 111.37 - 118.46: 3546 118.46 - 125.55: 5936 125.55 - 132.64: 909 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 2.440 nonbonded pdb=" OG SER C 842 " pdb=" O THR G1041 " model vdw 2.254 2.440 nonbonded pdb=" O ILE E 719 " pdb=" OG SER F 247 " model vdw 2.265 2.440 nonbonded pdb=" O GLY C 906 " pdb=" OG1 THR E 658 " model vdw 2.288 2.440 nonbonded pdb=" O SER C 916 " pdb=" OG SER C 916 " model vdw 2.298 2.440 ... (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 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: 0.400 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: 2.250 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.540 Find NCS groups from input model: 0.410 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.570 ------------------------------------------------------------------------------- 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= 0.398 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 346 time to evaluate : 0.841 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: 0.2957 time to fit residues: 137.7123 Evaluate side-chains 287 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 0.1980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1446 HIS H1481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12230 Z= 0.182 Angle : 0.604 7.124 17678 Z= 0.354 Chirality : 0.035 0.141 2019 Planarity : 0.004 0.055 1290 Dihedral : 31.387 174.359 3809 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 5.50 % Allowed : 22.33 % Favored : 72.17 % 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: 0.42 (0.30), residues: 730 helix: 1.43 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.97 (0.34), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE F 300 TYR 0.018 0.002 TYR D1318 ARG 0.012 0.001 ARG C 845 *********************** 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 355 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 321 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLN cc_start: 0.9047 (tt0) cc_final: 0.8762 (tm-30) REVERT: A 473 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8259 (tm-30) REVERT: A 485 GLN cc_start: 0.8852 (mt0) cc_final: 0.8413 (mt0) REVERT: A 520 MET cc_start: 0.8029 (mtt) cc_final: 0.7417 (mtp) REVERT: B 52 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8446 (tp30) REVERT: B 74 GLU cc_start: 0.9231 (tt0) cc_final: 0.9022 (tt0) REVERT: B 81 VAL cc_start: 0.9186 (t) cc_final: 0.8771 (p) REVERT: B 98 TYR cc_start: 0.9033 (m-10) cc_final: 0.8812 (m-80) REVERT: C 821 GLN cc_start: 0.9067 (mp10) cc_final: 0.8862 (mp10) REVERT: C 826 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7735 (mm110) REVERT: C 853 TYR cc_start: 0.8774 (t80) cc_final: 0.8190 (t80) REVERT: C 875 ASP cc_start: 0.8922 (m-30) cc_final: 0.8376 (p0) REVERT: C 884 ARG cc_start: 0.8796 (tpt170) cc_final: 0.8327 (tpt170) REVERT: C 887 GLN cc_start: 0.9096 (tp40) cc_final: 0.8805 (tp-100) REVERT: C 901 LYS cc_start: 0.8999 (pttp) cc_final: 0.8299 (tptp) REVERT: C 912 HIS cc_start: 0.8386 (t70) cc_final: 0.7820 (t-90) REVERT: D 1268 GLU cc_start: 0.9007 (tp30) cc_final: 0.8779 (tp30) REVERT: D 1276 ARG cc_start: 0.8613 (ttm110) cc_final: 0.8366 (ttm-80) REVERT: D 1279 HIS cc_start: 0.8711 (t-90) cc_final: 0.8102 (t70) REVERT: D 1281 ASN cc_start: 0.9342 (t0) cc_final: 0.8936 (t0) REVERT: D 1317 LYS cc_start: 0.9244 (ttmm) cc_final: 0.8956 (ttmt) REVERT: E 693 GLN cc_start: 0.8925 (tt0) cc_final: 0.8646 (tp40) REVERT: E 705 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8570 (tm-30) REVERT: E 722 LYS cc_start: 0.8750 (pttt) cc_final: 0.8523 (ptpp) REVERT: E 725 GLN cc_start: 0.9208 (mt0) cc_final: 0.8924 (mt0) REVERT: F 244 LYS cc_start: 0.9064 (tttt) cc_final: 0.8752 (tttt) REVERT: F 274 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8851 (tm-30) REVERT: F 284 MET cc_start: 0.8987 (tpp) cc_final: 0.8300 (mmm) REVERT: F 291 LYS cc_start: 0.8960 (tttp) cc_final: 0.8559 (ttpt) REVERT: G 1045 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8903 (ptm160) REVERT: G 1059 GLU cc_start: 0.8689 (tt0) cc_final: 0.8386 (tt0) REVERT: G 1084 ARG cc_start: 0.8842 (tpt170) cc_final: 0.8436 (tpp80) REVERT: G 1088 LEU cc_start: 0.9268 (mm) cc_final: 0.8912 (mm) REVERT: H 1461 SER cc_start: 0.9525 (t) cc_final: 0.9296 (t) REVERT: H 1465 ASP cc_start: 0.9199 (t70) cc_final: 0.8944 (t0) REVERT: H 1468 GLU cc_start: 0.8593 (tp30) cc_final: 0.8311 (tt0) REVERT: H 1486 ILE cc_start: 0.8993 (mt) cc_final: 0.8678 (mt) REVERT: H 1505 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8815 (mttt) outliers start: 34 outliers final: 22 residues processed: 329 average time/residue: 0.2895 time to fit residues: 126.0067 Evaluate side-chains 312 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 289 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1253 SER Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1045 ARG Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain H residue 1488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 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 655 GLN E 668 GLN G1033 HIS ** G1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12230 Z= 0.309 Angle : 0.633 7.530 17678 Z= 0.372 Chirality : 0.036 0.148 2019 Planarity : 0.004 0.051 1290 Dihedral : 31.341 173.811 3805 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 7.28 % Allowed : 26.70 % Favored : 66.02 % 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: 0.98 (0.31), residues: 730 helix: 1.82 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -3.00 (0.36), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 713 PHE 0.014 0.002 PHE D1267 TYR 0.020 0.002 TYR D1318 ARG 0.006 0.000 ARG G1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7967 (pp20) cc_final: 0.7352 (pp20) REVERT: A 473 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8326 (tm-30) REVERT: A 520 MET cc_start: 0.8221 (mtt) cc_final: 0.7476 (mtp) REVERT: B 74 GLU cc_start: 0.9301 (tt0) cc_final: 0.9081 (tt0) REVERT: C 821 GLN cc_start: 0.9156 (mp10) cc_final: 0.8899 (mp10) REVERT: C 853 TYR cc_start: 0.8777 (t80) cc_final: 0.8127 (t80) REVERT: C 875 ASP cc_start: 0.8973 (m-30) cc_final: 0.8398 (p0) REVERT: C 887 GLN cc_start: 0.9101 (tp40) cc_final: 0.8798 (tp-100) REVERT: C 901 LYS cc_start: 0.9028 (pttp) cc_final: 0.8446 (tptp) REVERT: C 912 HIS cc_start: 0.8502 (t70) cc_final: 0.7761 (t-90) REVERT: D 1265 ASP cc_start: 0.8635 (t0) cc_final: 0.8424 (t0) REVERT: D 1268 GLU cc_start: 0.9159 (tp30) cc_final: 0.8891 (tp30) REVERT: D 1281 ASN cc_start: 0.9356 (t0) cc_final: 0.9007 (t0) REVERT: D 1317 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8953 (ttmt) REVERT: E 690 MET cc_start: 0.9066 (mmm) cc_final: 0.8756 (tpp) REVERT: E 693 GLN cc_start: 0.8976 (tt0) cc_final: 0.8623 (tp40) REVERT: E 694 GLU cc_start: 0.8976 (tp30) cc_final: 0.8620 (tp30) REVERT: E 705 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8523 (tm-30) REVERT: E 720 MET cc_start: 0.8692 (tpp) cc_final: 0.7789 (mpp) REVERT: E 722 LYS cc_start: 0.8786 (pttt) cc_final: 0.8555 (ptpp) REVERT: E 733 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7663 (pt0) REVERT: F 244 LYS cc_start: 0.9101 (tttt) cc_final: 0.8741 (tttt) REVERT: F 274 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8755 (tm-30) REVERT: F 279 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8328 (mtpt) REVERT: G 1059 GLU cc_start: 0.8654 (tt0) cc_final: 0.8405 (tt0) REVERT: G 1077 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9113 (mmmt) REVERT: G 1084 ARG cc_start: 0.8852 (tpt170) cc_final: 0.8419 (tpp80) REVERT: G 1087 GLN cc_start: 0.9094 (tp40) cc_final: 0.8885 (tp40) REVERT: G 1088 LEU cc_start: 0.9228 (mm) cc_final: 0.8857 (mm) REVERT: H 1461 SER cc_start: 0.9557 (t) cc_final: 0.9324 (t) REVERT: H 1486 ILE cc_start: 0.9046 (mt) cc_final: 0.8753 (mt) REVERT: H 1505 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8784 (mmtp) outliers start: 45 outliers final: 34 residues processed: 298 average time/residue: 0.2704 time to fit residues: 109.5785 Evaluate side-chains 302 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1041 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1065 VAL Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1497 LEU Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ** G1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2437 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= 0.230 Angle : 0.606 7.973 17678 Z= 0.356 Chirality : 0.035 0.167 2019 Planarity : 0.004 0.049 1290 Dihedral : 31.164 173.808 3803 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.28 % Allowed : 30.26 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.32 (0.31), residues: 730 helix: 2.05 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.77 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 713 PHE 0.014 0.002 PHE B 61 TYR 0.028 0.002 TYR H1480 ARG 0.006 0.000 ARG G1031 *********************** 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 fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7896 (pp20) cc_final: 0.7238 (pp20) REVERT: A 467 PHE cc_start: 0.8856 (t80) cc_final: 0.8590 (t80) REVERT: A 473 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 520 MET cc_start: 0.8222 (mtt) cc_final: 0.7516 (mtp) REVERT: B 74 GLU cc_start: 0.9255 (tt0) cc_final: 0.9028 (tt0) REVERT: C 821 GLN cc_start: 0.9098 (mp10) cc_final: 0.8832 (mp10) REVERT: C 826 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8250 (mm-40) REVERT: C 853 TYR cc_start: 0.8723 (t80) cc_final: 0.8055 (t80) REVERT: C 867 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 875 ASP cc_start: 0.8951 (m-30) cc_final: 0.8414 (p0) REVERT: C 884 ARG cc_start: 0.8757 (tpt170) cc_final: 0.8287 (tpt170) REVERT: C 887 GLN cc_start: 0.9078 (tp40) cc_final: 0.8802 (tp-100) REVERT: C 901 LYS cc_start: 0.9003 (pttp) cc_final: 0.8428 (tptp) REVERT: C 912 HIS cc_start: 0.8487 (t70) cc_final: 0.7873 (t-90) REVERT: D 1265 ASP cc_start: 0.8666 (t0) cc_final: 0.8427 (t0) REVERT: D 1268 GLU cc_start: 0.9173 (tp30) cc_final: 0.8789 (tp30) REVERT: D 1281 ASN cc_start: 0.9331 (t0) cc_final: 0.8973 (t0) REVERT: D 1317 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8930 (ttmt) REVERT: E 690 MET cc_start: 0.9029 (mmm) cc_final: 0.8712 (tpp) REVERT: E 693 GLN cc_start: 0.8855 (tt0) cc_final: 0.8564 (tp40) REVERT: E 694 GLU cc_start: 0.8904 (tp30) cc_final: 0.8579 (tp30) REVERT: E 705 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8536 (tm-30) REVERT: E 720 MET cc_start: 0.8693 (tpp) cc_final: 0.7887 (mpp) REVERT: F 274 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8684 (tm-30) REVERT: F 279 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8377 (mtpt) REVERT: G 1021 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (pp30) REVERT: G 1045 ARG cc_start: 0.9305 (ptm160) cc_final: 0.8793 (ptm160) REVERT: G 1059 GLU cc_start: 0.8570 (tt0) cc_final: 0.8280 (tt0) REVERT: G 1077 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9115 (mmmt) REVERT: G 1084 ARG cc_start: 0.8857 (tpt170) cc_final: 0.8393 (tpp80) REVERT: G 1088 LEU cc_start: 0.9218 (mm) cc_final: 0.8804 (mm) REVERT: H 1468 GLU cc_start: 0.8707 (tp30) cc_final: 0.8482 (tt0) REVERT: H 1482 LYS cc_start: 0.9203 (mttt) cc_final: 0.8793 (mmtt) REVERT: H 1486 ILE cc_start: 0.8954 (mt) cc_final: 0.8583 (mt) REVERT: H 1490 GLU cc_start: 0.9204 (mp0) cc_final: 0.8870 (mp0) REVERT: H 1505 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8769 (mtmt) outliers start: 45 outliers final: 35 residues processed: 296 average time/residue: 0.2579 time to fit residues: 103.6066 Evaluate side-chains 299 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR 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 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain F residue 247 SER 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 297 LEU Chi-restraints excluded: chain G residue 1021 GLN Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain H residue 1477 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN G1021 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12230 Z= 0.300 Angle : 0.625 8.110 17678 Z= 0.368 Chirality : 0.036 0.176 2019 Planarity : 0.004 0.047 1290 Dihedral : 31.204 173.662 3803 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 9.55 % Allowed : 27.67 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.26 (0.31), residues: 730 helix: 1.98 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.015 0.002 PHE D1267 TYR 0.025 0.003 TYR B 88 ARG 0.005 0.000 ARG G1031 *********************** 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 323 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 264 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7851 (pp20) cc_final: 0.7228 (pp20) REVERT: A 468 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 473 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 520 MET cc_start: 0.8214 (mtt) cc_final: 0.7460 (mtp) REVERT: B 74 GLU cc_start: 0.9295 (tt0) cc_final: 0.9051 (tt0) REVERT: B 88 TYR cc_start: 0.8171 (m-80) cc_final: 0.7684 (m-80) REVERT: C 821 GLN cc_start: 0.9121 (mp10) cc_final: 0.8832 (mp10) REVERT: C 853 TYR cc_start: 0.8764 (t80) cc_final: 0.8110 (t80) REVERT: C 875 ASP cc_start: 0.8969 (m-30) cc_final: 0.8501 (p0) REVERT: C 887 GLN cc_start: 0.9077 (tp40) cc_final: 0.8790 (tp-100) REVERT: C 900 ILE cc_start: 0.8693 (mp) cc_final: 0.8492 (mp) REVERT: C 901 LYS cc_start: 0.9008 (pttp) cc_final: 0.8407 (tptp) REVERT: C 912 HIS cc_start: 0.8499 (t70) cc_final: 0.7895 (t-90) REVERT: D 1265 ASP cc_start: 0.8709 (t0) cc_final: 0.8453 (t0) REVERT: D 1268 GLU cc_start: 0.9166 (tp30) cc_final: 0.8687 (tp30) REVERT: D 1281 ASN cc_start: 0.9355 (t0) cc_final: 0.8996 (t0) REVERT: D 1317 LYS cc_start: 0.9235 (ttmm) cc_final: 0.8959 (ttmt) REVERT: E 668 GLN cc_start: 0.9118 (tt0) cc_final: 0.8016 (tm-30) REVERT: E 690 MET cc_start: 0.9027 (mmm) cc_final: 0.8681 (tpp) REVERT: E 693 GLN cc_start: 0.8908 (tt0) cc_final: 0.8627 (tp40) REVERT: E 705 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8539 (tm-30) REVERT: E 720 MET cc_start: 0.8710 (tpp) cc_final: 0.7853 (mpp) REVERT: E 733 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7572 (pt0) REVERT: F 244 LYS cc_start: 0.8982 (tttt) cc_final: 0.8397 (tttt) REVERT: F 274 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 279 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8183 (mtmt) REVERT: G 1045 ARG cc_start: 0.9333 (ptm160) cc_final: 0.8939 (ptm-80) REVERT: G 1059 GLU cc_start: 0.8590 (tt0) cc_final: 0.8247 (tt0) REVERT: G 1077 LYS cc_start: 0.9387 (mmmt) cc_final: 0.9149 (mmmt) REVERT: G 1084 ARG cc_start: 0.8846 (tpt170) cc_final: 0.8356 (tpp80) REVERT: G 1088 LEU cc_start: 0.9237 (mm) cc_final: 0.8829 (mm) REVERT: H 1482 LYS cc_start: 0.9220 (mttt) cc_final: 0.8797 (mmtt) REVERT: H 1486 ILE cc_start: 0.8880 (mt) cc_final: 0.8400 (mt) REVERT: H 1490 GLU cc_start: 0.9153 (mp0) cc_final: 0.8889 (mp0) REVERT: H 1505 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8753 (mtmt) outliers start: 59 outliers final: 54 residues processed: 290 average time/residue: 0.2706 time to fit residues: 106.4268 Evaluate side-chains 310 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 480 THR 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 C residue 852 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1285 THR Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1021 GLN Chi-restraints excluded: chain G residue 1041 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1065 VAL Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1485 THR Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1021 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12230 Z= 0.244 Angle : 0.615 9.381 17678 Z= 0.361 Chirality : 0.035 0.181 2019 Planarity : 0.004 0.048 1290 Dihedral : 31.146 173.808 3803 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 9.06 % Allowed : 30.42 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.33 (0.31), residues: 730 helix: 1.99 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -2.60 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 713 PHE 0.022 0.002 PHE A 467 TYR 0.026 0.002 TYR D1318 ARG 0.008 0.000 ARG D1296 *********************** 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 325 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7840 (pp20) cc_final: 0.7194 (pp20) REVERT: A 468 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: A 473 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 520 MET cc_start: 0.8240 (mtt) cc_final: 0.7523 (mtp) REVERT: B 74 GLU cc_start: 0.9279 (tt0) cc_final: 0.9047 (tt0) REVERT: B 88 TYR cc_start: 0.8241 (m-80) cc_final: 0.7919 (m-80) REVERT: C 821 GLN cc_start: 0.9095 (mp10) cc_final: 0.8814 (mp10) REVERT: C 853 TYR cc_start: 0.8530 (t80) cc_final: 0.7957 (t80) REVERT: C 867 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8818 (tm-30) REVERT: C 875 ASP cc_start: 0.8954 (m-30) cc_final: 0.8414 (p0) REVERT: C 884 ARG cc_start: 0.8756 (tpt170) cc_final: 0.8286 (tpt170) REVERT: C 887 GLN cc_start: 0.9071 (tp40) cc_final: 0.8803 (tp-100) REVERT: C 901 LYS cc_start: 0.8987 (pttp) cc_final: 0.8375 (tptp) REVERT: C 912 HIS cc_start: 0.8479 (t70) cc_final: 0.7899 (t-90) REVERT: D 1265 ASP cc_start: 0.8659 (t0) cc_final: 0.8397 (t0) REVERT: D 1268 GLU cc_start: 0.9151 (tp30) cc_final: 0.8654 (tp30) REVERT: D 1281 ASN cc_start: 0.9318 (t0) cc_final: 0.8945 (t0) REVERT: D 1317 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8960 (ttmt) REVERT: E 690 MET cc_start: 0.8954 (mmm) cc_final: 0.8645 (tpp) REVERT: E 693 GLN cc_start: 0.8869 (tt0) cc_final: 0.8508 (tp40) REVERT: E 705 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8554 (tm-30) REVERT: E 720 MET cc_start: 0.8786 (tpp) cc_final: 0.8157 (mpp) REVERT: E 733 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7586 (pt0) REVERT: F 244 LYS cc_start: 0.9002 (tttt) cc_final: 0.8364 (tttt) REVERT: F 250 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9466 (mm) REVERT: F 274 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8634 (tm-30) REVERT: F 279 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8188 (mtmt) REVERT: G 1017 VAL cc_start: 0.8405 (t) cc_final: 0.8171 (p) REVERT: G 1045 ARG cc_start: 0.9321 (ptm160) cc_final: 0.8886 (ptm160) REVERT: G 1059 GLU cc_start: 0.8535 (tt0) cc_final: 0.8200 (tt0) REVERT: G 1077 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9192 (mmmt) REVERT: G 1079 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8596 (ptmm) REVERT: G 1084 ARG cc_start: 0.8820 (tpt170) cc_final: 0.8303 (tpp80) REVERT: G 1088 LEU cc_start: 0.9208 (mm) cc_final: 0.8787 (mm) REVERT: H 1482 LYS cc_start: 0.9213 (mttt) cc_final: 0.8804 (mmtt) REVERT: H 1486 ILE cc_start: 0.8917 (mt) cc_final: 0.8507 (mt) REVERT: H 1490 GLU cc_start: 0.9172 (mp0) cc_final: 0.8776 (mp0) REVERT: H 1505 LYS cc_start: 0.9011 (tmmt) cc_final: 0.8737 (mtmt) outliers start: 56 outliers final: 47 residues processed: 291 average time/residue: 0.2592 time to fit residues: 103.4822 Evaluate side-chains 310 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 261 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 480 THR 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 B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1021 GLN Chi-restraints excluded: chain G residue 1041 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1433 SER Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 493 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12230 Z= 0.211 Angle : 0.606 9.978 17678 Z= 0.356 Chirality : 0.035 0.184 2019 Planarity : 0.004 0.049 1290 Dihedral : 31.104 173.922 3803 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 7.61 % Allowed : 32.52 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.40 (0.31), residues: 730 helix: 2.08 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.52 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 713 PHE 0.025 0.002 PHE A 467 TYR 0.022 0.002 TYR D1318 ARG 0.006 0.000 ARG D1296 *********************** 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 322 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7815 (pp20) cc_final: 0.7244 (pp20) REVERT: A 468 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: A 520 MET cc_start: 0.8197 (mtt) cc_final: 0.7486 (mtp) REVERT: A 533 GLU cc_start: 0.8142 (pt0) cc_final: 0.7941 (pt0) REVERT: B 74 GLU cc_start: 0.9271 (tt0) cc_final: 0.9035 (tt0) REVERT: B 88 TYR cc_start: 0.8227 (m-80) cc_final: 0.7883 (m-80) REVERT: C 821 GLN cc_start: 0.9101 (mp10) cc_final: 0.8807 (mp10) REVERT: C 822 ARG cc_start: 0.9196 (ttt-90) cc_final: 0.8434 (ttt90) REVERT: C 826 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8265 (mm-40) REVERT: C 853 TYR cc_start: 0.8563 (t80) cc_final: 0.8090 (t80) REVERT: C 875 ASP cc_start: 0.8942 (m-30) cc_final: 0.8477 (p0) REVERT: C 884 ARG cc_start: 0.8769 (tpt170) cc_final: 0.8317 (tpt170) REVERT: C 887 GLN cc_start: 0.9060 (tp40) cc_final: 0.8798 (tp-100) REVERT: C 901 LYS cc_start: 0.8972 (pttp) cc_final: 0.8436 (tptp) REVERT: C 912 HIS cc_start: 0.8458 (t70) cc_final: 0.7906 (t-90) REVERT: D 1231 LYS cc_start: 0.8798 (tppt) cc_final: 0.8431 (ptpt) REVERT: D 1265 ASP cc_start: 0.8664 (t0) cc_final: 0.8406 (t0) REVERT: D 1268 GLU cc_start: 0.9162 (tp30) cc_final: 0.8668 (tp30) REVERT: D 1279 HIS cc_start: 0.8816 (t-90) cc_final: 0.8459 (t70) REVERT: D 1281 ASN cc_start: 0.9295 (t0) cc_final: 0.8929 (t0) REVERT: D 1317 LYS cc_start: 0.9219 (ttmm) cc_final: 0.8942 (ttmt) REVERT: E 690 MET cc_start: 0.8869 (mmm) cc_final: 0.8562 (tpp) REVERT: E 693 GLN cc_start: 0.8767 (tt0) cc_final: 0.8441 (tp40) REVERT: E 705 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8510 (tm-30) REVERT: E 720 MET cc_start: 0.8821 (tpp) cc_final: 0.8238 (mpp) REVERT: E 733 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7515 (pt0) REVERT: F 244 LYS cc_start: 0.9013 (tttt) cc_final: 0.8259 (tttt) REVERT: F 250 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9406 (mm) REVERT: F 274 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8582 (tm-30) REVERT: F 279 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8190 (mtmt) REVERT: G 1017 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8133 (p) REVERT: G 1021 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (pp30) REVERT: G 1045 ARG cc_start: 0.9318 (ptm160) cc_final: 0.8879 (ptm160) REVERT: G 1059 GLU cc_start: 0.8509 (tt0) cc_final: 0.8234 (tt0) REVERT: G 1079 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8728 (ptmm) REVERT: G 1084 ARG cc_start: 0.8816 (tpt170) cc_final: 0.8277 (tpp80) REVERT: G 1088 LEU cc_start: 0.9228 (mm) cc_final: 0.8824 (mm) REVERT: H 1482 LYS cc_start: 0.9228 (mttt) cc_final: 0.8816 (mmtt) REVERT: H 1486 ILE cc_start: 0.8854 (mt) cc_final: 0.8372 (mt) REVERT: H 1490 GLU cc_start: 0.9182 (mp0) cc_final: 0.8743 (mp0) REVERT: H 1505 LYS cc_start: 0.8975 (tmmt) cc_final: 0.8692 (mtmt) outliers start: 47 outliers final: 39 residues processed: 293 average time/residue: 0.2643 time to fit residues: 105.8144 Evaluate side-chains 312 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 269 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN 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 B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 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 1263 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 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 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1477 LEU Chi-restraints excluded: chain H residue 1508 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1021 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 12230 Z= 0.247 Angle : 0.619 8.047 17678 Z= 0.363 Chirality : 0.035 0.187 2019 Planarity : 0.004 0.048 1290 Dihedral : 31.104 173.870 3803 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 8.09 % Allowed : 32.20 % Favored : 59.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.32 (0.31), residues: 730 helix: 2.01 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.54 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 713 PHE 0.015 0.002 PHE A 467 TYR 0.021 0.002 TYR D1318 ARG 0.006 0.000 ARG A 534 *********************** 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 328 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 278 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7758 (pp20) cc_final: 0.7133 (pp20) REVERT: A 460 LEU cc_start: 0.8432 (mm) cc_final: 0.7733 (mt) REVERT: A 468 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8907 (tm-30) REVERT: A 494 GLU cc_start: 0.8865 (tp30) cc_final: 0.8628 (tp30) REVERT: A 504 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: A 516 ARG cc_start: 0.8285 (mtm110) cc_final: 0.7184 (mtm-85) REVERT: A 520 MET cc_start: 0.8225 (mtt) cc_final: 0.7558 (mtp) REVERT: A 525 GLN cc_start: 0.8836 (mt0) cc_final: 0.8538 (mt0) REVERT: B 74 GLU cc_start: 0.9285 (tt0) cc_final: 0.9037 (tt0) REVERT: B 88 TYR cc_start: 0.8186 (m-10) cc_final: 0.7821 (m-80) REVERT: C 821 GLN cc_start: 0.9115 (mp10) cc_final: 0.8812 (mp10) REVERT: C 822 ARG cc_start: 0.9198 (ttt-90) cc_final: 0.8395 (ttt90) REVERT: C 853 TYR cc_start: 0.8567 (t80) cc_final: 0.8070 (t80) REVERT: C 867 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8818 (tm-30) REVERT: C 875 ASP cc_start: 0.8946 (m-30) cc_final: 0.8476 (p0) REVERT: C 884 ARG cc_start: 0.8777 (tpt170) cc_final: 0.8325 (tpt170) REVERT: C 887 GLN cc_start: 0.9069 (tp40) cc_final: 0.8805 (tp-100) REVERT: C 901 LYS cc_start: 0.8972 (pttp) cc_final: 0.8453 (tptp) REVERT: C 912 HIS cc_start: 0.8399 (t70) cc_final: 0.7862 (t-90) REVERT: D 1231 LYS cc_start: 0.8756 (tppt) cc_final: 0.8495 (ptpt) REVERT: D 1265 ASP cc_start: 0.8666 (t0) cc_final: 0.8397 (t0) REVERT: D 1268 GLU cc_start: 0.9159 (tp30) cc_final: 0.8657 (tp30) REVERT: D 1279 HIS cc_start: 0.8813 (t-90) cc_final: 0.8477 (t70) REVERT: D 1281 ASN cc_start: 0.9258 (t0) cc_final: 0.8884 (t0) REVERT: D 1317 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8933 (ttmt) REVERT: E 690 MET cc_start: 0.8870 (mmm) cc_final: 0.8569 (tpp) REVERT: E 693 GLN cc_start: 0.8811 (tt0) cc_final: 0.8473 (tp40) REVERT: E 705 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8654 (tm-30) REVERT: E 708 ASN cc_start: 0.9296 (t0) cc_final: 0.9050 (t0) REVERT: E 720 MET cc_start: 0.8832 (tpp) cc_final: 0.8224 (mpp) REVERT: E 733 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7409 (pt0) REVERT: F 250 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9378 (mm) REVERT: F 274 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8572 (tm-30) REVERT: F 279 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8192 (mtmt) REVERT: F 284 MET cc_start: 0.8538 (mmm) cc_final: 0.8176 (mmm) REVERT: G 1045 ARG cc_start: 0.9317 (ptm160) cc_final: 0.8876 (ptm160) REVERT: G 1059 GLU cc_start: 0.8550 (tt0) cc_final: 0.8233 (tt0) REVERT: G 1079 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8723 (ptmm) REVERT: G 1084 ARG cc_start: 0.8853 (tpt170) cc_final: 0.8175 (tpp80) REVERT: G 1088 LEU cc_start: 0.9232 (mm) cc_final: 0.8829 (mm) REVERT: H 1482 LYS cc_start: 0.9240 (mttt) cc_final: 0.8828 (mmtt) REVERT: H 1486 ILE cc_start: 0.8879 (mt) cc_final: 0.8464 (mt) REVERT: H 1505 LYS cc_start: 0.8994 (tmmt) cc_final: 0.8725 (mtmt) outliers start: 50 outliers final: 43 residues processed: 299 average time/residue: 0.2716 time to fit residues: 109.2178 Evaluate side-chains 314 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 504 PHE 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 93 GLN Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1277 LEU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1319 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 710 CYS Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1021 GLN Chi-restraints excluded: chain G residue 1041 THR Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Chi-restraints excluded: chain G residue 1054 SER Chi-restraints excluded: chain G residue 1068 LEU Chi-restraints excluded: chain H residue 1477 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12230 Z= 0.193 Angle : 0.606 8.545 17678 Z= 0.355 Chirality : 0.035 0.192 2019 Planarity : 0.004 0.050 1290 Dihedral : 31.039 173.980 3803 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.02 % Allowed : 35.60 % Favored : 59.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.46 (0.31), residues: 730 helix: 2.08 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.36 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 713 PHE 0.008 0.001 PHE A 467 TYR 0.019 0.002 TYR D1318 ARG 0.008 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 289 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7732 (pp20) cc_final: 0.7163 (pp20) REVERT: A 460 LEU cc_start: 0.8323 (mm) cc_final: 0.7687 (mt) REVERT: A 467 PHE cc_start: 0.8188 (t80) cc_final: 0.7985 (t80) REVERT: A 468 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 494 GLU cc_start: 0.8824 (tp30) cc_final: 0.8588 (tp30) REVERT: A 504 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: A 516 ARG cc_start: 0.8216 (mtm110) cc_final: 0.6962 (mtm-85) REVERT: A 520 MET cc_start: 0.8221 (mtt) cc_final: 0.7557 (mtp) REVERT: A 525 GLN cc_start: 0.8786 (mt0) cc_final: 0.8499 (mt0) REVERT: A 528 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.7563 (mtp-110) REVERT: B 88 TYR cc_start: 0.8157 (m-10) cc_final: 0.7807 (m-80) REVERT: C 821 GLN cc_start: 0.9131 (mp10) cc_final: 0.8811 (mp10) REVERT: C 822 ARG cc_start: 0.9089 (ttt-90) cc_final: 0.8362 (ttt90) REVERT: C 826 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8229 (mm-40) REVERT: C 831 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8317 (ttm110) REVERT: C 853 TYR cc_start: 0.8538 (t80) cc_final: 0.8140 (t80) REVERT: C 867 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8746 (tm-30) REVERT: C 875 ASP cc_start: 0.8912 (m-30) cc_final: 0.8455 (p0) REVERT: C 884 ARG cc_start: 0.8757 (tpt170) cc_final: 0.8329 (tpt170) REVERT: C 887 GLN cc_start: 0.9080 (tp40) cc_final: 0.8830 (tp-100) REVERT: C 901 LYS cc_start: 0.8942 (pttp) cc_final: 0.8452 (tptp) REVERT: C 912 HIS cc_start: 0.8386 (t70) cc_final: 0.7829 (t-90) REVERT: D 1265 ASP cc_start: 0.8636 (t0) cc_final: 0.8383 (t0) REVERT: D 1268 GLU cc_start: 0.9091 (tp30) cc_final: 0.8589 (tp30) REVERT: D 1279 HIS cc_start: 0.8808 (t-90) cc_final: 0.8460 (t70) REVERT: D 1281 ASN cc_start: 0.9149 (t0) cc_final: 0.8803 (t0) REVERT: D 1317 LYS cc_start: 0.9196 (ttmm) cc_final: 0.8918 (ttmt) REVERT: E 676 GLN cc_start: 0.8828 (tp40) cc_final: 0.8553 (tp40) REVERT: E 693 GLN cc_start: 0.8777 (tt0) cc_final: 0.8419 (tp40) REVERT: E 720 MET cc_start: 0.8913 (tpp) cc_final: 0.8210 (mpp) REVERT: F 243 VAL cc_start: 0.9366 (p) cc_final: 0.9161 (p) REVERT: F 244 LYS cc_start: 0.8953 (tttt) cc_final: 0.8183 (tttt) REVERT: F 274 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8488 (tm-30) REVERT: F 279 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8155 (mtmt) REVERT: G 1021 GLN cc_start: 0.8718 (pt0) cc_final: 0.8344 (pp30) REVERT: G 1045 ARG cc_start: 0.9303 (ptm160) cc_final: 0.8894 (ptm160) REVERT: G 1059 GLU cc_start: 0.8506 (tt0) cc_final: 0.8195 (tt0) REVERT: G 1084 ARG cc_start: 0.8837 (tpt170) cc_final: 0.8162 (tpp80) REVERT: G 1088 LEU cc_start: 0.9157 (mm) cc_final: 0.8877 (mm) REVERT: H 1482 LYS cc_start: 0.9243 (mttt) cc_final: 0.8839 (mmtt) REVERT: H 1486 ILE cc_start: 0.8757 (mt) cc_final: 0.8436 (mt) REVERT: H 1505 LYS cc_start: 0.9007 (tmmt) cc_final: 0.8790 (mttt) outliers start: 31 outliers final: 23 residues processed: 300 average time/residue: 0.2655 time to fit residues: 108.3620 Evaluate side-chains 307 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 282 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1241 VAL Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain G residue 1049 THR Chi-restraints excluded: chain G residue 1052 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 64 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3299 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= 0.181 Angle : 0.606 10.442 17678 Z= 0.353 Chirality : 0.035 0.258 2019 Planarity : 0.004 0.052 1290 Dihedral : 30.995 174.098 3803 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.56 % Allowed : 37.06 % Favored : 59.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.41 (0.31), residues: 730 helix: 2.01 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 275 PHE 0.013 0.001 PHE A 467 TYR 0.019 0.002 TYR D1318 ARG 0.008 0.000 ARG A 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7681 (pp20) cc_final: 0.7114 (pp20) REVERT: A 460 LEU cc_start: 0.8294 (mm) cc_final: 0.7713 (mt) REVERT: A 468 GLN cc_start: 0.9117 (tt0) cc_final: 0.8728 (tm-30) REVERT: A 494 GLU cc_start: 0.8829 (tp30) cc_final: 0.8584 (tp30) REVERT: A 504 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: A 516 ARG cc_start: 0.8279 (mtm110) cc_final: 0.6996 (mtm-85) REVERT: A 520 MET cc_start: 0.8170 (mtt) cc_final: 0.7498 (mtp) REVERT: A 525 GLN cc_start: 0.8804 (mt0) cc_final: 0.8600 (mt0) REVERT: A 528 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.8030 (mtm180) REVERT: B 53 GLU cc_start: 0.9232 (tp30) cc_final: 0.8983 (tp30) REVERT: B 88 TYR cc_start: 0.8141 (m-10) cc_final: 0.7787 (m-80) REVERT: C 821 GLN cc_start: 0.9147 (mp10) cc_final: 0.8807 (mp10) REVERT: C 822 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8303 (ttt90) REVERT: C 826 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8204 (mm-40) REVERT: C 853 TYR cc_start: 0.8510 (t80) cc_final: 0.8113 (t80) REVERT: C 867 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8748 (tm-30) REVERT: C 875 ASP cc_start: 0.8889 (m-30) cc_final: 0.8444 (p0) REVERT: C 884 ARG cc_start: 0.8737 (tpt170) cc_final: 0.8308 (tpt170) REVERT: C 887 GLN cc_start: 0.9070 (tp40) cc_final: 0.8833 (tp-100) REVERT: C 901 LYS cc_start: 0.8897 (pttp) cc_final: 0.8417 (tptp) REVERT: C 912 HIS cc_start: 0.8339 (t70) cc_final: 0.7816 (t-90) REVERT: D 1229 THR cc_start: 0.6933 (t) cc_final: 0.6614 (t) REVERT: D 1265 ASP cc_start: 0.8651 (t0) cc_final: 0.8441 (t0) REVERT: D 1268 GLU cc_start: 0.9070 (tp30) cc_final: 0.8541 (tp30) REVERT: D 1279 HIS cc_start: 0.8809 (t-90) cc_final: 0.8483 (t70) REVERT: D 1281 ASN cc_start: 0.9072 (t0) cc_final: 0.8770 (t0) REVERT: D 1317 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8904 (ttmt) REVERT: E 676 GLN cc_start: 0.8771 (tp40) cc_final: 0.8465 (tp40) REVERT: E 693 GLN cc_start: 0.8768 (tt0) cc_final: 0.8414 (tp40) REVERT: E 708 ASN cc_start: 0.9151 (t0) cc_final: 0.8912 (t0) REVERT: E 720 MET cc_start: 0.8922 (tpp) cc_final: 0.8201 (mpp) REVERT: F 237 LEU cc_start: 0.9335 (tp) cc_final: 0.9097 (tt) REVERT: F 244 LYS cc_start: 0.8929 (tttt) cc_final: 0.8146 (tttt) REVERT: F 274 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8444 (tm-30) REVERT: F 279 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8156 (mtmt) REVERT: G 1021 GLN cc_start: 0.8605 (pt0) cc_final: 0.8249 (pp30) REVERT: G 1045 ARG cc_start: 0.9284 (ptm160) cc_final: 0.8846 (ptm160) REVERT: G 1059 GLU cc_start: 0.8475 (tt0) cc_final: 0.8188 (tt0) REVERT: G 1084 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8190 (tpp80) REVERT: G 1088 LEU cc_start: 0.9135 (mm) cc_final: 0.8863 (mm) REVERT: H 1468 GLU cc_start: 0.8746 (tp30) cc_final: 0.8518 (tt0) REVERT: H 1482 LYS cc_start: 0.9199 (mttt) cc_final: 0.8826 (mmtt) REVERT: H 1486 ILE cc_start: 0.8800 (mt) cc_final: 0.8518 (mt) outliers start: 22 outliers final: 20 residues processed: 299 average time/residue: 0.2837 time to fit residues: 114.3702 Evaluate side-chains 301 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 280 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 504 PHE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain D residue 1282 LYS Chi-restraints excluded: chain D residue 1287 THR Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 1049 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.098275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071291 restraints weight = 33124.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073422 restraints weight = 16563.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074852 restraints weight = 11180.103| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12230 Z= 0.288 Angle : 0.638 8.991 17678 Z= 0.371 Chirality : 0.036 0.221 2019 Planarity : 0.004 0.049 1290 Dihedral : 31.098 173.530 3803 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.21 % Allowed : 37.38 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.33 (0.31), residues: 730 helix: 1.97 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.36 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.032 0.002 PHE A 467 TYR 0.031 0.002 TYR F 288 ARG 0.008 0.001 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.44 seconds wall clock time: 45 minutes 51.67 seconds (2751.67 seconds total)