Starting phenix.real_space_refine on Tue Jun 10 16:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.map" model { file = "/net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gy0_51680/06_2025/9gy0_51680.cif" } resolution = 3.42 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 64 5.49 5 S 72 5.16 5 C 7297 2.51 5 N 2042 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11866 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4816 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 605 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1964 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1812 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain breaks: 3 Chain: "G" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P DG B 21 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG B 21 " occ=0.00 Time building chain proxies: 8.00, per 1000 atoms: 0.67 Number of scatterers: 11866 At special positions: 0 Unit cell: (105.133, 104.219, 144.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 72 16.00 P 64 15.00 O 2390 8.00 N 2042 7.00 C 7297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 162 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 40.9% alpha, 19.8% beta 27 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.512A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 411 through 424 removed outlier: 3.755A pdb=" N ARG A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.678A pdb=" N GLU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.932A pdb=" N GLN A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.546A pdb=" N VAL A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 4.552A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 598 through 622 Processing helix chain 'A' and resid 623 through 642 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.592A pdb=" N HIS A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 681 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.533A pdb=" N SER A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 722 through 735 Processing helix chain 'A' and resid 740 through 755 removed outlier: 3.865A pdb=" N LEU A 746 " --> pdb=" O HIS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 813 through 825 Processing helix chain 'A' and resid 834 through 851 removed outlier: 4.063A pdb=" N PHE A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 removed outlier: 3.801A pdb=" N ARG A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.678A pdb=" N ASP A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 909 Processing helix chain 'A' and resid 924 through 949 removed outlier: 6.172A pdb=" N GLY A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Proline residue: A 938 - end of helix Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'E' and resid 9 through 23 removed outlier: 3.564A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.837A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.570A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 57 Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 141 through 155 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 783 removed outlier: 4.156A pdb=" N LYS A 778 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 970 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 963 " --> pdb=" O LYS A 972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62 removed outlier: 5.496A pdb=" N THR E 59 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG E 5 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG E 61 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN G 177 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.430A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET E 229 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS E 135 " --> pdb=" O MET E 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 204 through 208 removed outlier: 5.747A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.540A pdb=" N ALA F 26 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AB1, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.563A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 177 through 181 removed outlier: 3.704A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.930A pdb=" N PHE G 2 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 40 removed outlier: 4.580A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 159 552 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2023 1.32 - 1.45: 3279 1.45 - 1.57: 6662 1.57 - 1.69: 126 1.69 - 1.81: 111 Bond restraints: 12201 Sorted by residual: bond pdb=" C MET F 68 " pdb=" N GLY F 69 " ideal model delta sigma weight residual 1.331 1.409 -0.079 1.46e-02 4.69e+03 2.90e+01 bond pdb=" C ALA F 67 " pdb=" N MET F 68 " ideal model delta sigma weight residual 1.333 1.262 0.070 1.42e-02 4.96e+03 2.46e+01 bond pdb=" CA SER A 825 " pdb=" CB SER A 825 " ideal model delta sigma weight residual 1.531 1.463 0.068 1.69e-02 3.50e+03 1.60e+01 bond pdb=" C VAL G 236 " pdb=" N VAL G 237 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" C TRP A 707 " pdb=" O TRP A 707 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.04e+00 ... (remaining 12196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 16248 1.64 - 3.27: 421 3.27 - 4.91: 76 4.91 - 6.55: 16 6.55 - 8.19: 6 Bond angle restraints: 16767 Sorted by residual: angle pdb=" C ALA G 67 " pdb=" N MET G 68 " pdb=" CA MET G 68 " ideal model delta sigma weight residual 122.36 114.17 8.19 1.42e+00 4.96e-01 3.32e+01 angle pdb=" N LEU A 713 " pdb=" CA LEU A 713 " pdb=" C LEU A 713 " ideal model delta sigma weight residual 111.69 106.58 5.11 1.23e+00 6.61e-01 1.73e+01 angle pdb=" CA TRP A 707 " pdb=" C TRP A 707 " pdb=" O TRP A 707 " ideal model delta sigma weight residual 120.42 116.03 4.39 1.06e+00 8.90e-01 1.71e+01 angle pdb=" N MET G 68 " pdb=" CA MET G 68 " pdb=" C MET G 68 " ideal model delta sigma weight residual 111.39 105.75 5.64 1.38e+00 5.25e-01 1.67e+01 angle pdb=" N VAL G 237 " pdb=" CA VAL G 237 " pdb=" C VAL G 237 " ideal model delta sigma weight residual 108.11 102.45 5.66 1.40e+00 5.10e-01 1.64e+01 ... (remaining 16762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5862 17.64 - 35.28: 858 35.28 - 52.93: 394 52.93 - 70.57: 92 70.57 - 88.21: 11 Dihedral angle restraints: 7217 sinusoidal: 3310 harmonic: 3907 Sorted by residual: dihedral pdb=" CB CYS G 135 " pdb=" SG CYS G 135 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual 93.00 45.21 47.79 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CA HIS A 681 " pdb=" C HIS A 681 " pdb=" N MET A 682 " pdb=" CA MET A 682 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C LEU G 118 " pdb=" N LEU G 118 " pdb=" CA LEU G 118 " pdb=" CB LEU G 118 " ideal model delta harmonic sigma weight residual -122.60 -112.86 -9.74 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 7214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1868 0.104 - 0.208: 58 0.208 - 0.313: 2 0.313 - 0.417: 0 0.417 - 0.521: 3 Chirality restraints: 1931 Sorted by residual: chirality pdb=" P DT C 22 " pdb=" OP1 DT C 22 " pdb=" OP2 DT C 22 " pdb=" O5' DT C 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" P DT C 21 " pdb=" OP1 DT C 21 " pdb=" OP2 DT C 21 " pdb=" O5' DT C 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA LEU G 118 " pdb=" N LEU G 118 " pdb=" C LEU G 118 " pdb=" CB LEU G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 1928 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 706 " 0.218 9.50e-02 1.11e+02 9.80e-02 5.91e+00 pdb=" NE ARG A 706 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 706 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 706 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 706 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 114 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C TYR G 114 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR G 114 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU G 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 704 " -0.169 9.50e-02 1.11e+02 7.57e-02 3.52e+00 pdb=" NE ARG A 704 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 704 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 704 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 704 " -0.006 2.00e-02 2.50e+03 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 348 2.70 - 3.25: 11421 3.25 - 3.80: 19621 3.80 - 4.35: 24494 4.35 - 4.90: 39917 Nonbonded interactions: 95801 Sorted by model distance: nonbonded pdb=" O2 DC B 36 " pdb=" N2 DG C 5 " model vdw 2.148 2.496 nonbonded pdb=" OG SER G 46 " pdb=" O TYR G 250 " model vdw 2.203 3.040 nonbonded pdb=" NE2 HIS A 718 " pdb=" OP1 DC B 17 " model vdw 2.248 3.120 nonbonded pdb=" OG SER G 222 " pdb=" O THR G 224 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 396 " pdb=" NZ LYS A 401 " model vdw 2.251 3.120 ... (remaining 95796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'F' and resid 1 through 253) selection = (chain 'G' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ h 185 or resid 193 through 253)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.810 Find NCS groups from input model: 0.370 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.004 0.079 12202 Z= 0.218 Angle : 0.635 8.187 16769 Z= 0.379 Chirality : 0.046 0.521 1931 Planarity : 0.004 0.098 1913 Dihedral : 19.963 88.211 4670 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.21 % Allowed : 28.09 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.24), residues: 1319 helix: 1.32 (0.25), residues: 481 sheet: 0.15 (0.28), residues: 341 loop : -1.00 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 708 HIS 0.007 0.001 HIS A 970 PHE 0.024 0.001 PHE F 144 TYR 0.009 0.001 TYR A 418 ARG 0.006 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.13478 ( 622) hydrogen bonds : angle 5.60268 ( 1712) SS BOND : bond 0.00590 ( 1) SS BOND : angle 0.88712 ( 2) covalent geometry : bond 0.00356 (12201) covalent geometry : angle 0.63448 (16767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.196 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 581 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7720 (mtm110) REVERT: A 648 ARG cc_start: 0.7539 (mpt180) cc_final: 0.6777 (mmt180) REVERT: A 670 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 764 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6981 (m170) REVERT: A 950 ASP cc_start: 0.8229 (t70) cc_final: 0.7810 (t70) REVERT: E 116 MET cc_start: 0.7687 (mtp) cc_final: 0.7391 (mtp) REVERT: E 151 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7160 (mp) REVERT: E 240 LYS cc_start: 0.8173 (mttt) cc_final: 0.7620 (mmtm) REVERT: F 1 MET cc_start: 0.7663 (ppp) cc_final: 0.7311 (tmm) REVERT: F 30 ILE cc_start: 0.6765 (tp) cc_final: 0.6401 (mm) REVERT: F 49 GLN cc_start: 0.6182 (tp40) cc_final: 0.4782 (tm-30) REVERT: F 146 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7714 (mmm160) REVERT: F 168 LYS cc_start: 0.8279 (mttt) cc_final: 0.7940 (mptt) REVERT: F 199 MET cc_start: 0.5196 (ptp) cc_final: 0.4943 (mmm) REVERT: F 215 PHE cc_start: 0.6758 (m-10) cc_final: 0.6000 (m-80) REVERT: F 248 LYS cc_start: 0.5975 (mttt) cc_final: 0.5053 (tttm) REVERT: G 151 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7171 (mm) REVERT: G 229 MET cc_start: 0.4954 (mpp) cc_final: 0.4176 (mpp) outliers start: 26 outliers final: 19 residues processed: 173 average time/residue: 0.2923 time to fit residues: 69.6290 Evaluate side-chains 162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 764 HIS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN E 71 ASN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS G 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.177417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127308 restraints weight = 18524.130| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.53 r_work: 0.3427 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 12202 Z= 0.261 Angle : 0.638 8.423 16769 Z= 0.335 Chirality : 0.044 0.156 1931 Planarity : 0.004 0.044 1913 Dihedral : 18.930 72.049 2143 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.47 % Allowed : 24.26 % Favored : 69.28 % 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: 0.05 (0.23), residues: 1319 helix: 1.14 (0.24), residues: 496 sheet: 0.22 (0.28), residues: 344 loop : -1.24 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 847 HIS 0.006 0.001 HIS A1005 PHE 0.019 0.002 PHE F 144 TYR 0.019 0.002 TYR E 211 ARG 0.005 0.001 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 622) hydrogen bonds : angle 4.94749 ( 1712) SS BOND : bond 0.00637 ( 1) SS BOND : angle 1.31333 ( 2) covalent geometry : bond 0.00625 (12201) covalent geometry : angle 0.63766 (16767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8185 (mtpt) REVERT: A 498 ASP cc_start: 0.8764 (m-30) cc_final: 0.8329 (m-30) REVERT: A 648 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7018 (mmt180) REVERT: A 869 ASP cc_start: 0.8713 (m-30) cc_final: 0.8500 (m-30) REVERT: A 909 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: A 910 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: A 982 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8558 (mtm110) REVERT: E 2 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.5795 (p90) REVERT: E 116 MET cc_start: 0.7755 (mtp) cc_final: 0.7271 (mtp) REVERT: E 179 ASN cc_start: 0.6888 (p0) cc_final: 0.6457 (p0) REVERT: E 240 LYS cc_start: 0.8169 (mttt) cc_final: 0.7560 (mmtm) REVERT: F 1 MET cc_start: 0.7739 (ppp) cc_final: 0.7318 (tmm) REVERT: F 30 ILE cc_start: 0.6744 (tp) cc_final: 0.6375 (mm) REVERT: F 146 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7754 (mmm160) REVERT: F 168 LYS cc_start: 0.8035 (mttt) cc_final: 0.7654 (mptt) REVERT: F 199 MET cc_start: 0.5195 (ptp) cc_final: 0.4948 (mmm) REVERT: F 215 PHE cc_start: 0.6580 (m-10) cc_final: 0.5794 (m-80) REVERT: F 248 LYS cc_start: 0.5753 (mttt) cc_final: 0.5060 (tttm) REVERT: G 75 MET cc_start: 0.6885 (ttt) cc_final: 0.5827 (mmp) REVERT: G 119 MET cc_start: 0.5562 (tmm) cc_final: 0.5254 (tmm) REVERT: G 229 MET cc_start: 0.4906 (mpp) cc_final: 0.4191 (mpp) outliers start: 76 outliers final: 49 residues processed: 208 average time/residue: 0.2607 time to fit residues: 75.4599 Evaluate side-chains 190 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 232 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132483 restraints weight = 18409.318| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.51 r_work: 0.3474 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12202 Z= 0.130 Angle : 0.547 7.728 16769 Z= 0.287 Chirality : 0.041 0.152 1931 Planarity : 0.003 0.039 1913 Dihedral : 18.715 71.249 2122 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.34 % Allowed : 26.55 % Favored : 69.11 % 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: 0.27 (0.23), residues: 1319 helix: 1.49 (0.24), residues: 497 sheet: 0.22 (0.28), residues: 331 loop : -1.19 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 707 HIS 0.004 0.001 HIS E 44 PHE 0.008 0.001 PHE F 169 TYR 0.016 0.002 TYR E 211 ARG 0.006 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 622) hydrogen bonds : angle 4.60133 ( 1712) SS BOND : bond 0.00471 ( 1) SS BOND : angle 0.87145 ( 2) covalent geometry : bond 0.00296 (12201) covalent geometry : angle 0.54668 (16767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8725 (m-30) cc_final: 0.8355 (m-30) REVERT: A 648 ARG cc_start: 0.7528 (mpt180) cc_final: 0.6889 (mmt180) REVERT: A 649 CYS cc_start: 0.8924 (t) cc_final: 0.8590 (t) REVERT: A 670 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7617 (mp) REVERT: A 765 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6648 (tp) REVERT: A 869 ASP cc_start: 0.8685 (m-30) cc_final: 0.8387 (m-30) REVERT: E 2 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.5916 (p90) REVERT: E 116 MET cc_start: 0.7725 (mtp) cc_final: 0.7353 (mtp) REVERT: E 179 ASN cc_start: 0.6817 (p0) cc_final: 0.6571 (p0) REVERT: E 240 LYS cc_start: 0.8145 (mttt) cc_final: 0.7516 (mmtm) REVERT: F 1 MET cc_start: 0.7769 (ppp) cc_final: 0.7369 (tmm) REVERT: F 30 ILE cc_start: 0.6726 (tp) cc_final: 0.6430 (mm) REVERT: F 146 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7689 (mmm160) REVERT: F 168 LYS cc_start: 0.8040 (mttt) cc_final: 0.7663 (mptt) REVERT: F 199 MET cc_start: 0.5207 (ptp) cc_final: 0.4751 (mmm) REVERT: F 215 PHE cc_start: 0.6597 (m-10) cc_final: 0.5838 (m-80) REVERT: F 248 LYS cc_start: 0.5775 (mttt) cc_final: 0.5111 (tttm) REVERT: G 75 MET cc_start: 0.6867 (ttt) cc_final: 0.5873 (mmp) REVERT: G 229 MET cc_start: 0.4796 (mpp) cc_final: 0.4201 (mpp) outliers start: 51 outliers final: 31 residues processed: 193 average time/residue: 0.2743 time to fit residues: 73.3137 Evaluate side-chains 182 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 0.0000 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130587 restraints weight = 18408.616| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.35 r_work: 0.3511 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12202 Z= 0.114 Angle : 0.515 7.062 16769 Z= 0.272 Chirality : 0.040 0.146 1931 Planarity : 0.003 0.036 1913 Dihedral : 18.575 70.076 2114 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.51 % Allowed : 27.40 % Favored : 68.09 % 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: 0.46 (0.23), residues: 1319 helix: 1.75 (0.24), residues: 496 sheet: 0.34 (0.29), residues: 325 loop : -1.19 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 707 HIS 0.004 0.001 HIS E 44 PHE 0.023 0.001 PHE F 144 TYR 0.016 0.001 TYR E 211 ARG 0.006 0.000 ARG F 5 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 622) hydrogen bonds : angle 4.37512 ( 1712) SS BOND : bond 0.00460 ( 1) SS BOND : angle 0.82849 ( 2) covalent geometry : bond 0.00251 (12201) covalent geometry : angle 0.51469 (16767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: A 498 ASP cc_start: 0.8733 (m-30) cc_final: 0.8377 (m-30) REVERT: A 648 ARG cc_start: 0.7490 (mpt180) cc_final: 0.6924 (mmt180) REVERT: A 649 CYS cc_start: 0.8860 (t) cc_final: 0.8511 (t) REVERT: A 670 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 765 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6736 (tp) REVERT: A 869 ASP cc_start: 0.8663 (m-30) cc_final: 0.8326 (m-30) REVERT: E 2 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.5930 (p90) REVERT: E 116 MET cc_start: 0.7729 (mtp) cc_final: 0.7412 (mtp) REVERT: E 179 ASN cc_start: 0.6571 (p0) cc_final: 0.6363 (p0) REVERT: E 198 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: E 240 LYS cc_start: 0.8164 (mttt) cc_final: 0.7543 (mmtm) REVERT: F 30 ILE cc_start: 0.6676 (tp) cc_final: 0.6429 (mm) REVERT: F 49 GLN cc_start: 0.6118 (tp40) cc_final: 0.4690 (tm-30) REVERT: F 146 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7688 (mmm160) REVERT: F 168 LYS cc_start: 0.8064 (mttt) cc_final: 0.7617 (mptt) REVERT: F 199 MET cc_start: 0.5207 (ptp) cc_final: 0.4796 (mmm) REVERT: F 248 LYS cc_start: 0.5732 (mttt) cc_final: 0.4889 (tttm) REVERT: G 75 MET cc_start: 0.6795 (ttt) cc_final: 0.5841 (mmp) outliers start: 53 outliers final: 32 residues processed: 207 average time/residue: 0.3177 time to fit residues: 91.4097 Evaluate side-chains 189 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 62 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135487 restraints weight = 18581.078| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.34 r_work: 0.3529 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12202 Z= 0.121 Angle : 0.519 6.957 16769 Z= 0.273 Chirality : 0.040 0.139 1931 Planarity : 0.003 0.035 1913 Dihedral : 18.552 69.374 2114 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.94 % Allowed : 26.89 % Favored : 68.17 % 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: 0.52 (0.23), residues: 1319 helix: 1.83 (0.24), residues: 496 sheet: 0.28 (0.28), residues: 323 loop : -1.13 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 708 HIS 0.004 0.001 HIS E 44 PHE 0.008 0.001 PHE F 169 TYR 0.015 0.001 TYR E 211 ARG 0.006 0.000 ARG F 5 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 622) hydrogen bonds : angle 4.35835 ( 1712) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.70566 ( 2) covalent geometry : bond 0.00273 (12201) covalent geometry : angle 0.51849 (16767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8062 (mtmt) REVERT: A 498 ASP cc_start: 0.8793 (m-30) cc_final: 0.8424 (m-30) REVERT: A 592 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8440 (mmtt) REVERT: A 648 ARG cc_start: 0.7617 (mpt180) cc_final: 0.7037 (mmt180) REVERT: A 649 CYS cc_start: 0.9018 (t) cc_final: 0.8698 (t) REVERT: A 670 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 869 ASP cc_start: 0.8754 (m-30) cc_final: 0.8430 (m-30) REVERT: E 2 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.5937 (p90) REVERT: E 116 MET cc_start: 0.7756 (mtp) cc_final: 0.7331 (mtp) REVERT: E 179 ASN cc_start: 0.6760 (p0) cc_final: 0.6481 (p0) REVERT: E 198 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5767 (pp20) REVERT: E 240 LYS cc_start: 0.8241 (mttt) cc_final: 0.7632 (mmtm) REVERT: F 5 ARG cc_start: 0.6595 (ttm-80) cc_final: 0.6327 (ttm-80) REVERT: F 30 ILE cc_start: 0.6648 (tp) cc_final: 0.6423 (mm) REVERT: F 49 GLN cc_start: 0.6267 (tp40) cc_final: 0.4796 (tm-30) REVERT: F 146 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7681 (mmm-85) REVERT: F 168 LYS cc_start: 0.8111 (mttt) cc_final: 0.7667 (mptt) REVERT: F 199 MET cc_start: 0.5276 (ptp) cc_final: 0.4841 (mmm) REVERT: F 215 PHE cc_start: 0.6525 (m-10) cc_final: 0.5737 (m-80) REVERT: F 248 LYS cc_start: 0.5857 (mttt) cc_final: 0.5022 (tttm) REVERT: G 75 MET cc_start: 0.6696 (ttt) cc_final: 0.5728 (mmp) REVERT: G 199 MET cc_start: 0.3903 (mmp) cc_final: 0.0828 (tmm) REVERT: G 229 MET cc_start: 0.4589 (mpp) cc_final: 0.3858 (mpp) outliers start: 58 outliers final: 37 residues processed: 197 average time/residue: 0.3838 time to fit residues: 106.6680 Evaluate side-chains 190 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141563 restraints weight = 18494.317| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.27 r_work: 0.3420 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12202 Z= 0.127 Angle : 0.522 7.392 16769 Z= 0.273 Chirality : 0.040 0.138 1931 Planarity : 0.003 0.035 1913 Dihedral : 18.550 68.809 2114 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.11 % Allowed : 26.47 % Favored : 68.43 % 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: 0.57 (0.23), residues: 1319 helix: 1.88 (0.24), residues: 497 sheet: 0.28 (0.28), residues: 334 loop : -1.12 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.004 0.001 HIS E 44 PHE 0.009 0.001 PHE F 169 TYR 0.015 0.002 TYR E 211 ARG 0.006 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 622) hydrogen bonds : angle 4.34464 ( 1712) SS BOND : bond 0.00510 ( 1) SS BOND : angle 0.79718 ( 2) covalent geometry : bond 0.00290 (12201) covalent geometry : angle 0.52195 (16767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (mtpt) REVERT: A 424 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7711 (mtm-85) REVERT: A 498 ASP cc_start: 0.8767 (m-30) cc_final: 0.8404 (m-30) REVERT: A 592 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8466 (mmtt) REVERT: A 648 ARG cc_start: 0.7611 (mpt180) cc_final: 0.7031 (mmt180) REVERT: A 649 CYS cc_start: 0.8855 (t) cc_final: 0.8494 (t) REVERT: A 670 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 869 ASP cc_start: 0.8757 (m-30) cc_final: 0.8407 (m-30) REVERT: E 2 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6016 (p90) REVERT: E 41 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8064 (p0) REVERT: E 116 MET cc_start: 0.7775 (mtp) cc_final: 0.7360 (mtp) REVERT: E 198 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5763 (pp20) REVERT: E 240 LYS cc_start: 0.8269 (mttt) cc_final: 0.7664 (mmtm) REVERT: F 30 ILE cc_start: 0.6641 (tp) cc_final: 0.6423 (mm) REVERT: F 49 GLN cc_start: 0.6256 (tp40) cc_final: 0.4772 (tm-30) REVERT: F 146 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7689 (mmm-85) REVERT: F 168 LYS cc_start: 0.8099 (mttt) cc_final: 0.7648 (mptt) REVERT: F 199 MET cc_start: 0.5246 (ptp) cc_final: 0.4822 (mmm) REVERT: F 221 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5353 (tt) REVERT: F 238 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.3448 (tm-30) REVERT: F 248 LYS cc_start: 0.5759 (mttt) cc_final: 0.4976 (tttm) REVERT: G 75 MET cc_start: 0.6754 (ttt) cc_final: 0.5669 (mmp) outliers start: 60 outliers final: 45 residues processed: 194 average time/residue: 0.3138 time to fit residues: 83.9907 Evaluate side-chains 197 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143109 restraints weight = 18338.963| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.30 r_work: 0.3432 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12202 Z= 0.113 Angle : 0.511 7.171 16769 Z= 0.268 Chirality : 0.039 0.139 1931 Planarity : 0.003 0.034 1913 Dihedral : 18.503 67.864 2114 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.70 % Allowed : 25.87 % Favored : 68.43 % 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: 0.64 (0.23), residues: 1319 helix: 1.97 (0.24), residues: 497 sheet: 0.29 (0.28), residues: 334 loop : -1.10 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.003 0.001 HIS E 44 PHE 0.008 0.001 PHE F 169 TYR 0.014 0.001 TYR E 211 ARG 0.007 0.000 ARG F 5 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 622) hydrogen bonds : angle 4.26007 ( 1712) SS BOND : bond 0.00409 ( 1) SS BOND : angle 0.61807 ( 2) covalent geometry : bond 0.00252 (12201) covalent geometry : angle 0.51092 (16767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: A 424 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7713 (mtm-85) REVERT: A 464 GLU cc_start: 0.8240 (tp30) cc_final: 0.7895 (mm-30) REVERT: A 498 ASP cc_start: 0.8757 (m-30) cc_final: 0.8397 (m-30) REVERT: A 512 TRP cc_start: 0.5752 (p90) cc_final: 0.3795 (m-90) REVERT: A 592 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8398 (mmtt) REVERT: A 648 ARG cc_start: 0.7645 (mpt180) cc_final: 0.6980 (mmt180) REVERT: A 649 CYS cc_start: 0.8804 (t) cc_final: 0.8452 (t) REVERT: A 670 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7626 (mp) REVERT: A 869 ASP cc_start: 0.8739 (m-30) cc_final: 0.8372 (m-30) REVERT: A 880 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7462 (ttp-110) REVERT: A 950 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8105 (t70) REVERT: E 2 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.5968 (p90) REVERT: E 41 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (p0) REVERT: E 91 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7691 (mtp180) REVERT: E 116 MET cc_start: 0.7735 (mtp) cc_final: 0.7418 (mtp) REVERT: E 198 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5747 (pp20) REVERT: E 240 LYS cc_start: 0.8260 (mttt) cc_final: 0.7652 (mmtm) REVERT: F 30 ILE cc_start: 0.6660 (tp) cc_final: 0.6446 (mm) REVERT: F 49 GLN cc_start: 0.6284 (tp40) cc_final: 0.4830 (tm-30) REVERT: F 146 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7700 (mmm-85) REVERT: F 168 LYS cc_start: 0.8063 (mttt) cc_final: 0.7645 (mptt) REVERT: F 199 MET cc_start: 0.5145 (ptp) cc_final: 0.4770 (mmm) REVERT: F 215 PHE cc_start: 0.6509 (m-10) cc_final: 0.5729 (m-80) REVERT: F 238 GLU cc_start: 0.3845 (OUTLIER) cc_final: 0.3529 (tm-30) REVERT: F 248 LYS cc_start: 0.5797 (mttt) cc_final: 0.5103 (tttm) REVERT: G 75 MET cc_start: 0.6760 (ttt) cc_final: 0.5645 (mmp) REVERT: G 214 PHE cc_start: 0.7020 (m-80) cc_final: 0.6752 (m-10) REVERT: G 229 MET cc_start: 0.4326 (mpp) cc_final: 0.3322 (mpp) outliers start: 67 outliers final: 46 residues processed: 209 average time/residue: 0.3414 time to fit residues: 100.4759 Evaluate side-chains 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 44 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141582 restraints weight = 18299.140| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.51 r_work: 0.3405 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12202 Z= 0.136 Angle : 0.534 8.466 16769 Z= 0.279 Chirality : 0.040 0.160 1931 Planarity : 0.003 0.035 1913 Dihedral : 18.532 67.691 2114 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 26.21 % Favored : 68.60 % 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: 0.58 (0.23), residues: 1319 helix: 1.91 (0.24), residues: 496 sheet: 0.29 (0.28), residues: 334 loop : -1.15 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.005 0.001 HIS E 44 PHE 0.013 0.001 PHE A 596 TYR 0.015 0.002 TYR E 211 ARG 0.007 0.000 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 622) hydrogen bonds : angle 4.32515 ( 1712) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.67250 ( 2) covalent geometry : bond 0.00316 (12201) covalent geometry : angle 0.53375 (16767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: A 424 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.7687 (mtm-85) REVERT: A 464 GLU cc_start: 0.8303 (tp30) cc_final: 0.7975 (mm-30) REVERT: A 498 ASP cc_start: 0.8767 (m-30) cc_final: 0.8397 (m-30) REVERT: A 592 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8439 (mmtt) REVERT: A 648 ARG cc_start: 0.7619 (mpt180) cc_final: 0.6961 (mmt180) REVERT: A 649 CYS cc_start: 0.8895 (t) cc_final: 0.8530 (t) REVERT: A 670 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 869 ASP cc_start: 0.8784 (m-30) cc_final: 0.8448 (m-30) REVERT: A 880 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7520 (ttp-110) REVERT: E 2 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6003 (p90) REVERT: E 41 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7991 (p0) REVERT: E 116 MET cc_start: 0.7770 (mtp) cc_final: 0.7392 (mtp) REVERT: E 198 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5753 (pp20) REVERT: E 240 LYS cc_start: 0.8281 (mttt) cc_final: 0.7665 (mmtm) REVERT: F 30 ILE cc_start: 0.6661 (tp) cc_final: 0.6447 (mm) REVERT: F 49 GLN cc_start: 0.6304 (tp40) cc_final: 0.4853 (tm-30) REVERT: F 146 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7760 (mmm160) REVERT: F 168 LYS cc_start: 0.7984 (mttt) cc_final: 0.7425 (mppt) REVERT: F 199 MET cc_start: 0.5201 (ptp) cc_final: 0.4787 (mmm) REVERT: F 215 PHE cc_start: 0.6604 (m-10) cc_final: 0.5785 (m-80) REVERT: F 221 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5379 (tt) REVERT: F 238 GLU cc_start: 0.3923 (OUTLIER) cc_final: 0.3600 (tm-30) REVERT: F 248 LYS cc_start: 0.5854 (mttt) cc_final: 0.5144 (tttm) REVERT: G 75 MET cc_start: 0.6805 (ttt) cc_final: 0.5666 (mmp) REVERT: G 214 PHE cc_start: 0.7043 (m-80) cc_final: 0.6761 (m-10) REVERT: G 229 MET cc_start: 0.4492 (mpp) cc_final: 0.3523 (mpp) outliers start: 61 outliers final: 46 residues processed: 196 average time/residue: 0.3713 time to fit residues: 103.0249 Evaluate side-chains 199 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 44 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 184 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.181398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142215 restraints weight = 18427.676| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.57 r_work: 0.3414 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12202 Z= 0.125 Angle : 0.534 8.474 16769 Z= 0.280 Chirality : 0.040 0.141 1931 Planarity : 0.003 0.034 1913 Dihedral : 18.511 67.116 2114 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.94 % Allowed : 26.81 % Favored : 68.26 % 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: 0.60 (0.23), residues: 1319 helix: 1.94 (0.24), residues: 497 sheet: 0.25 (0.28), residues: 332 loop : -1.12 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.006 0.001 HIS E 44 PHE 0.009 0.001 PHE F 169 TYR 0.015 0.001 TYR E 211 ARG 0.007 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 622) hydrogen bonds : angle 4.29396 ( 1712) SS BOND : bond 0.00449 ( 1) SS BOND : angle 0.65585 ( 2) covalent geometry : bond 0.00285 (12201) covalent geometry : angle 0.53373 (16767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (mtpt) REVERT: A 424 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7698 (mtm-85) REVERT: A 464 GLU cc_start: 0.8291 (tp30) cc_final: 0.7959 (mm-30) REVERT: A 498 ASP cc_start: 0.8764 (m-30) cc_final: 0.8397 (m-30) REVERT: A 592 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8436 (mmtt) REVERT: A 648 ARG cc_start: 0.7662 (mpt180) cc_final: 0.6994 (mmt180) REVERT: A 649 CYS cc_start: 0.8853 (t) cc_final: 0.8504 (t) REVERT: A 670 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 715 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 869 ASP cc_start: 0.8764 (m-30) cc_final: 0.8422 (m-30) REVERT: A 880 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7542 (ttp-110) REVERT: A 950 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (t70) REVERT: E 2 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.5877 (p90) REVERT: E 41 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7992 (p0) REVERT: E 99 LEU cc_start: 0.6243 (tp) cc_final: 0.6028 (tp) REVERT: E 116 MET cc_start: 0.7731 (mtp) cc_final: 0.7404 (mtp) REVERT: E 198 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5764 (pp20) REVERT: E 240 LYS cc_start: 0.8292 (mttt) cc_final: 0.7695 (mmtm) REVERT: F 49 GLN cc_start: 0.6347 (tp40) cc_final: 0.4902 (tm-30) REVERT: F 146 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7765 (mmm160) REVERT: F 168 LYS cc_start: 0.7981 (mttt) cc_final: 0.7503 (mmtm) REVERT: F 199 MET cc_start: 0.5217 (ptp) cc_final: 0.4782 (mmm) REVERT: F 215 PHE cc_start: 0.6615 (m-10) cc_final: 0.5809 (m-80) REVERT: F 221 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5449 (tt) REVERT: F 238 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.3637 (tm-30) REVERT: F 248 LYS cc_start: 0.5880 (mttt) cc_final: 0.5182 (tttm) REVERT: G 75 MET cc_start: 0.6763 (ttt) cc_final: 0.5566 (mmp) REVERT: G 201 GLU cc_start: 0.5518 (pp20) cc_final: 0.4079 (pm20) REVERT: G 214 PHE cc_start: 0.7087 (m-80) cc_final: 0.6789 (m-10) REVERT: G 229 MET cc_start: 0.4382 (mpp) cc_final: 0.3455 (mpp) outliers start: 58 outliers final: 45 residues processed: 192 average time/residue: 0.2804 time to fit residues: 73.4433 Evaluate side-chains 200 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 44 HIS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.182158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143284 restraints weight = 18410.053| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.36 r_work: 0.3441 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12202 Z= 0.115 Angle : 0.529 8.184 16769 Z= 0.277 Chirality : 0.040 0.140 1931 Planarity : 0.003 0.034 1913 Dihedral : 18.461 66.359 2114 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.68 % Allowed : 27.06 % Favored : 68.26 % 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: 0.65 (0.23), residues: 1319 helix: 1.99 (0.24), residues: 497 sheet: 0.29 (0.28), residues: 326 loop : -1.09 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.005 0.001 HIS E 44 PHE 0.031 0.001 PHE A 762 TYR 0.015 0.001 TYR E 211 ARG 0.007 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 622) hydrogen bonds : angle 4.25296 ( 1712) SS BOND : bond 0.00391 ( 1) SS BOND : angle 0.57612 ( 2) covalent geometry : bond 0.00258 (12201) covalent geometry : angle 0.52897 (16767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7996 (mtpt) REVERT: A 424 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.7681 (mtm-85) REVERT: A 464 GLU cc_start: 0.8251 (tp30) cc_final: 0.7933 (mm-30) REVERT: A 498 ASP cc_start: 0.8742 (m-30) cc_final: 0.8366 (m-30) REVERT: A 512 TRP cc_start: 0.5730 (p90) cc_final: 0.3847 (m-90) REVERT: A 592 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8396 (mmtt) REVERT: A 648 ARG cc_start: 0.7648 (mpt180) cc_final: 0.6996 (mmt180) REVERT: A 649 CYS cc_start: 0.8776 (t) cc_final: 0.8422 (t) REVERT: A 670 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 715 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8006 (mp) REVERT: A 880 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: A 950 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8106 (t70) REVERT: E 2 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.5899 (p90) REVERT: E 41 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7938 (p0) REVERT: E 91 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7760 (mtp180) REVERT: E 116 MET cc_start: 0.7675 (mtp) cc_final: 0.7346 (mtp) REVERT: E 198 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5782 (pp20) REVERT: E 240 LYS cc_start: 0.8278 (mttt) cc_final: 0.7671 (mmtm) REVERT: F 49 GLN cc_start: 0.6322 (tp40) cc_final: 0.4885 (tm-30) REVERT: F 146 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7763 (mmm-85) REVERT: F 168 LYS cc_start: 0.8014 (mttt) cc_final: 0.7576 (mptt) REVERT: F 199 MET cc_start: 0.5124 (ptp) cc_final: 0.4729 (mmm) REVERT: F 215 PHE cc_start: 0.6568 (m-10) cc_final: 0.5760 (m-80) REVERT: F 238 GLU cc_start: 0.3950 (OUTLIER) cc_final: 0.3659 (tm-30) REVERT: F 248 LYS cc_start: 0.5907 (mttt) cc_final: 0.5192 (tttm) REVERT: G 75 MET cc_start: 0.6790 (ttt) cc_final: 0.5613 (mmp) REVERT: G 199 MET cc_start: 0.3571 (mmp) cc_final: 0.0601 (tmm) REVERT: G 201 GLU cc_start: 0.5503 (pp20) cc_final: 0.4429 (pm20) REVERT: G 214 PHE cc_start: 0.7070 (m-80) cc_final: 0.6764 (m-10) REVERT: G 229 MET cc_start: 0.4443 (mpp) cc_final: 0.3625 (mpp) outliers start: 55 outliers final: 44 residues processed: 192 average time/residue: 0.2853 time to fit residues: 75.0109 Evaluate side-chains 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 44 HIS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.181269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135515 restraints weight = 18385.756| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.33 r_work: 0.3527 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12202 Z= 0.132 Angle : 0.544 8.489 16769 Z= 0.284 Chirality : 0.041 0.260 1931 Planarity : 0.003 0.034 1913 Dihedral : 18.484 66.062 2114 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.77 % Allowed : 27.32 % Favored : 67.91 % 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: 0.60 (0.23), residues: 1319 helix: 1.93 (0.24), residues: 497 sheet: 0.30 (0.28), residues: 326 loop : -1.13 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.005 0.001 HIS E 44 PHE 0.027 0.001 PHE A 762 TYR 0.015 0.002 TYR E 211 ARG 0.007 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 622) hydrogen bonds : angle 4.31205 ( 1712) SS BOND : bond 0.00417 ( 1) SS BOND : angle 0.58524 ( 2) covalent geometry : bond 0.00303 (12201) covalent geometry : angle 0.54409 (16767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7008.64 seconds wall clock time: 125 minutes 29.77 seconds (7529.77 seconds total)