Starting phenix.real_space_refine on Wed Jun 11 07:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.map" model { file = "/net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t90_10406/06_2025/6t90_10406.cif" } resolution = 3.05 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= 0.007 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 280 5.49 5 S 22 5.16 5 C 7345 2.51 5 N 2431 2.21 5 O 2953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13031 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2870 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "J" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2905 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 593 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "L" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 636 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.52, per 1000 atoms: 0.65 Number of scatterers: 13031 At special positions: 0 Unit cell: (97.18, 117.82, 141.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 280 15.00 O 2953 8.00 N 2431 7.00 C 7345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 74.6% alpha, 2.2% beta 141 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.521A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.825A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.959A pdb=" N GLY C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.324A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.517A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.551A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.746A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.071A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 160 Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 193 through 210 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 46 through 63 removed outlier: 3.630A pdb=" N GLY L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 Processing helix chain 'L' and resid 83 through 105 Proline residue: L 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.816A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.026A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.655A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.846A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.125A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 495 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2245 1.32 - 1.45: 5458 1.45 - 1.58: 5540 1.58 - 1.71: 547 1.71 - 1.84: 34 Bond restraints: 13824 Sorted by residual: bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.330 0.128 1.40e-02 5.10e+03 8.37e+01 bond pdb=" CD ARG B 36 " pdb=" NE ARG B 36 " ideal model delta sigma weight residual 1.458 1.359 0.099 1.40e-02 5.10e+03 5.02e+01 bond pdb=" CD ARG B 79 " pdb=" NE ARG B 79 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.91e+01 bond pdb=" CD ARG F 40 " pdb=" NE ARG F 40 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.86e+01 bond pdb=" CB HIS G 83 " pdb=" CG HIS G 83 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.82e+01 ... (remaining 13819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 17059 2.11 - 4.23: 2384 4.23 - 6.34: 355 6.34 - 8.46: 29 8.46 - 10.57: 5 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N LEU D 107 " pdb=" CA LEU D 107 " pdb=" C LEU D 107 " ideal model delta sigma weight residual 111.36 103.05 8.31 1.09e+00 8.42e-01 5.81e+01 angle pdb=" N LYS A 65 " pdb=" CA LYS A 65 " pdb=" C LYS A 65 " ideal model delta sigma weight residual 111.36 119.62 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" N GLY L 54 " pdb=" CA GLY L 54 " pdb=" C GLY L 54 " ideal model delta sigma weight residual 112.49 103.43 9.06 1.21e+00 6.83e-01 5.61e+01 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 111.36 119.51 -8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N LYS C 16 " pdb=" CA LYS C 16 " pdb=" C LYS C 16 " ideal model delta sigma weight residual 111.71 120.24 -8.53 1.15e+00 7.56e-01 5.50e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.28: 6426 33.28 - 66.56: 1201 66.56 - 99.84: 12 99.84 - 133.13: 0 133.13 - 166.41: 2 Dihedral angle restraints: 7641 sinusoidal: 5027 harmonic: 2614 Sorted by residual: dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 53.59 166.41 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 4 " pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " pdb=" P DA I 5 " ideal model delta sinusoidal sigma weight residual 220.00 57.11 162.89 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 7638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1228 0.070 - 0.139: 713 0.139 - 0.209: 247 0.209 - 0.279: 47 0.279 - 0.349: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASN L 68 " pdb=" N ASN L 68 " pdb=" C ASN L 68 " pdb=" CB ASN L 68 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA SER L 52 " pdb=" N SER L 52 " pdb=" C SER L 52 " pdb=" CB SER L 52 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2237 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.030 2.00e-02 2.50e+03 6.16e-02 3.80e+01 pdb=" C GLY B 103 " -0.107 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.039 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 103 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLY F 103 " 0.086 2.00e-02 2.50e+03 pdb=" O GLY F 103 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY F 103 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 207 " -0.047 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP K 207 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP K 207 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP K 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 207 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 207 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 207 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 207 " -0.023 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 5241 2.95 - 3.44: 11069 3.44 - 3.92: 24541 3.92 - 4.41: 29390 4.41 - 4.90: 37969 Nonbonded interactions: 108210 Sorted by model distance: nonbonded pdb=" OG1 THR F 83 " pdb=" N ALA F 84 " model vdw 2.459 3.120 nonbonded pdb=" OG1 THR B 83 " pdb=" N ALA B 84 " model vdw 2.469 3.120 nonbonded pdb=" OP1 DA J 139 " pdb=" NH2 ARG L 53 " model vdw 2.471 3.120 nonbonded pdb=" CB GLU E 98 " pdb=" OE1 GLU E 98 " model vdw 2.479 2.752 nonbonded pdb=" O ALA C 11 " pdb=" CG ARG C 12 " model vdw 2.493 3.440 ... (remaining 108205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 41 through 134 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and resid 23 through 103) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or resid 201)) selection = (chain 'G' and (resid 10 through 117 or resid 201)) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 37.860 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.023 0.178 13842 Z= 1.287 Angle : 1.522 10.572 19832 Z= 1.013 Chirality : 0.093 0.349 2240 Planarity : 0.008 0.062 1530 Dihedral : 24.655 166.407 5953 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 883 helix: 0.80 (0.18), residues: 647 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP K 207 HIS 0.008 0.002 HIS G 32 PHE 0.030 0.005 PHE L 90 TYR 0.047 0.008 TYR B 52 ARG 0.008 0.001 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.16252 ( 850) hydrogen bonds : angle 5.39970 ( 2171) covalent geometry : bond 0.02194 (13824) covalent geometry : angle 1.52209 (19832) Misc. bond : bond 0.16611 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8602 (pp20) REVERT: G 39 ASN cc_start: 0.7242 (m-40) cc_final: 0.6613 (m110) REVERT: K 163 THR cc_start: 0.7350 (p) cc_final: 0.7104 (p) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3321 time to fit residues: 97.7502 Evaluate side-chains 156 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 74 ASN D 85 ASN D 110 HIS G 32 HIS G 39 ASN H 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062236 restraints weight = 37983.729| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.21 r_work: 0.2874 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13842 Z= 0.186 Angle : 0.620 10.148 19832 Z= 0.367 Chirality : 0.036 0.183 2240 Planarity : 0.004 0.032 1530 Dihedral : 28.485 179.781 4128 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.92 % Allowed : 6.08 % Favored : 93.00 % 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: 3.02 (0.27), residues: 883 helix: 2.54 (0.19), residues: 669 sheet: None (None), residues: 0 loop : 0.28 (0.35), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 51 HIS 0.003 0.001 HIS G 83 PHE 0.021 0.002 PHE K 187 TYR 0.016 0.002 TYR H 41 ARG 0.008 0.001 ARG L 98 Details of bonding type rmsd hydrogen bonds : bond 0.05531 ( 850) hydrogen bonds : angle 3.10659 ( 2171) covalent geometry : bond 0.00394 (13824) covalent geometry : angle 0.61969 (19832) Misc. bond : bond 0.00087 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 223 time to evaluate : 1.365 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8674 (pm20) cc_final: 0.8445 (pm20) REVERT: E 124 ASP cc_start: 0.9083 (m-30) cc_final: 0.8872 (m-30) REVERT: F 26 ASN cc_start: 0.8732 (m-40) cc_final: 0.8452 (m-40) REVERT: F 89 TYR cc_start: 0.9169 (m-80) cc_final: 0.8942 (m-80) REVERT: H 94 GLU cc_start: 0.8866 (mp0) cc_final: 0.8653 (mp0) outliers start: 7 outliers final: 3 residues processed: 227 average time/residue: 0.4814 time to fit residues: 149.7591 Evaluate side-chains 179 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 0.0040 chunk 52 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN C 25 GLN E 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063300 restraints weight = 37707.289| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.26 r_work: 0.2902 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13842 Z= 0.148 Angle : 0.552 9.971 19832 Z= 0.328 Chirality : 0.033 0.141 2240 Planarity : 0.004 0.041 1530 Dihedral : 28.440 175.975 4128 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.45 % Allowed : 9.38 % Favored : 89.17 % 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: 3.36 (0.28), residues: 883 helix: 2.86 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.07 (0.36), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 51 HIS 0.004 0.001 HIS L 101 PHE 0.022 0.001 PHE K 187 TYR 0.013 0.001 TYR H 84 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 850) hydrogen bonds : angle 2.88645 ( 2171) covalent geometry : bond 0.00312 (13824) covalent geometry : angle 0.55152 (19832) Misc. bond : bond 0.00010 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.002 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: C 92 GLU cc_start: 0.8404 (pm20) cc_final: 0.8178 (pm20) REVERT: D 102 LEU cc_start: 0.9559 (mm) cc_final: 0.9354 (mm) REVERT: F 26 ASN cc_start: 0.8718 (m-40) cc_final: 0.8347 (m-40) REVERT: F 45 LYS cc_start: 0.8588 (tttt) cc_final: 0.8319 (ttmt) REVERT: F 89 TYR cc_start: 0.9140 (m-80) cc_final: 0.8936 (m-80) REVERT: G 91 ASP cc_start: 0.8730 (t0) cc_final: 0.8435 (t70) REVERT: G 111 ASN cc_start: 0.8030 (m-40) cc_final: 0.7767 (m110) REVERT: H 94 GLU cc_start: 0.8849 (mp0) cc_final: 0.8551 (mp0) outliers start: 11 outliers final: 5 residues processed: 201 average time/residue: 0.2816 time to fit residues: 78.3506 Evaluate side-chains 180 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 40 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 126 GLN C 39 ASN G 39 ASN H 110 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058748 restraints weight = 36829.695| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.22 r_work: 0.2784 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13842 Z= 0.228 Angle : 0.602 15.247 19832 Z= 0.348 Chirality : 0.036 0.127 2240 Planarity : 0.004 0.039 1530 Dihedral : 28.816 174.859 4128 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.38 % Allowed : 10.30 % Favored : 87.32 % 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: 3.28 (0.28), residues: 883 helix: 2.89 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 51 HIS 0.004 0.001 HIS L 101 PHE 0.019 0.002 PHE K 187 TYR 0.011 0.002 TYR H 41 ARG 0.006 0.001 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 850) hydrogen bonds : angle 3.15930 ( 2171) covalent geometry : bond 0.00517 (13824) covalent geometry : angle 0.60165 (19832) Misc. bond : bond 0.00018 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.199 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8546 (pm20) cc_final: 0.8119 (pm20) REVERT: C 93 GLU cc_start: 0.8900 (mp0) cc_final: 0.8683 (mp0) REVERT: D 102 LEU cc_start: 0.9511 (mm) cc_final: 0.9272 (mm) REVERT: D 106 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7414 (mm-30) REVERT: D 109 LYS cc_start: 0.8679 (tttt) cc_final: 0.8390 (tttt) REVERT: G 111 ASN cc_start: 0.8091 (m-40) cc_final: 0.7738 (p0) REVERT: H 122 TYR cc_start: 0.9250 (t80) cc_final: 0.9023 (t80) outliers start: 18 outliers final: 11 residues processed: 189 average time/residue: 0.2678 time to fit residues: 71.1043 Evaluate side-chains 184 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060454 restraints weight = 37478.292| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.23 r_work: 0.2830 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13842 Z= 0.169 Angle : 0.555 9.651 19832 Z= 0.329 Chirality : 0.033 0.135 2240 Planarity : 0.004 0.040 1530 Dihedral : 28.631 171.664 4128 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.11 % Allowed : 11.89 % Favored : 86.00 % 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: 3.36 (0.28), residues: 883 helix: 2.96 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 51 HIS 0.002 0.001 HIS B 76 PHE 0.022 0.001 PHE K 187 TYR 0.013 0.001 TYR H 84 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 850) hydrogen bonds : angle 2.98057 ( 2171) covalent geometry : bond 0.00370 (13824) covalent geometry : angle 0.55518 (19832) Misc. bond : bond 0.00007 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.102 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8551 (pm20) cc_final: 0.8075 (pm20) REVERT: C 39 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8527 (t0) REVERT: D 102 LEU cc_start: 0.9508 (mm) cc_final: 0.9276 (mm) REVERT: G 111 ASN cc_start: 0.8005 (m-40) cc_final: 0.7776 (p0) outliers start: 16 outliers final: 13 residues processed: 188 average time/residue: 0.2588 time to fit residues: 69.2031 Evaluate side-chains 183 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 40.0000 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 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 = 0.3857 r_free = 0.3857 target = 0.096719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059514 restraints weight = 37493.764| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.23 r_work: 0.2805 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13842 Z= 0.194 Angle : 0.573 13.119 19832 Z= 0.336 Chirality : 0.034 0.142 2240 Planarity : 0.004 0.042 1530 Dihedral : 28.734 170.076 4128 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.04 % Allowed : 11.76 % Favored : 85.20 % 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: 3.31 (0.28), residues: 883 helix: 2.92 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 51 HIS 0.003 0.001 HIS B 76 PHE 0.029 0.002 PHE K 187 TYR 0.016 0.001 TYR H 122 ARG 0.007 0.000 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 850) hydrogen bonds : angle 3.06028 ( 2171) covalent geometry : bond 0.00437 (13824) covalent geometry : angle 0.57323 (19832) Misc. bond : bond 0.00010 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.142 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: symmetry clash REVERT: A 60 GLU cc_start: 0.8523 (pm20) cc_final: 0.8042 (pm20) REVERT: C 92 GLU cc_start: 0.8596 (pm20) cc_final: 0.8333 (pm20) REVERT: C 93 GLU cc_start: 0.8919 (mp0) cc_final: 0.8300 (mp0) REVERT: D 94 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8679 (mp0) REVERT: D 102 LEU cc_start: 0.9504 (mm) cc_final: 0.9267 (mm) REVERT: D 109 LYS cc_start: 0.8674 (tttt) cc_final: 0.8450 (tttt) REVERT: G 91 ASP cc_start: 0.8766 (t0) cc_final: 0.8459 (t70) REVERT: G 111 ASN cc_start: 0.8088 (m-40) cc_final: 0.7881 (p0) REVERT: K 145 GLU cc_start: 0.8992 (tt0) cc_final: 0.8754 (tm-30) outliers start: 23 outliers final: 17 residues processed: 179 average time/residue: 0.2732 time to fit residues: 68.9930 Evaluate side-chains 185 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 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 = 0.3860 r_free = 0.3860 target = 0.097320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059533 restraints weight = 37401.489| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.30 r_work: 0.2797 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13842 Z= 0.190 Angle : 0.572 12.491 19832 Z= 0.335 Chirality : 0.034 0.147 2240 Planarity : 0.004 0.041 1530 Dihedral : 28.695 169.565 4128 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.64 % Allowed : 12.15 % Favored : 85.20 % 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: 3.25 (0.28), residues: 883 helix: 2.89 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 51 HIS 0.003 0.001 HIS B 76 PHE 0.027 0.002 PHE K 187 TYR 0.019 0.001 TYR H 84 ARG 0.006 0.000 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 850) hydrogen bonds : angle 3.06770 ( 2171) covalent geometry : bond 0.00425 (13824) covalent geometry : angle 0.57193 (19832) Misc. bond : bond 0.00009 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.949 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8494 (pm20) cc_final: 0.8005 (pm20) REVERT: C 92 GLU cc_start: 0.8636 (pm20) cc_final: 0.8292 (pm20) REVERT: C 93 GLU cc_start: 0.9014 (mp0) cc_final: 0.8275 (mp0) REVERT: D 94 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: D 102 LEU cc_start: 0.9502 (mm) cc_final: 0.9277 (mm) REVERT: D 109 LYS cc_start: 0.8631 (tttt) cc_final: 0.8394 (tttt) REVERT: E 60 GLU cc_start: 0.8409 (pm20) cc_final: 0.7997 (pm20) REVERT: G 20 SER cc_start: 0.9628 (t) cc_final: 0.9259 (p) REVERT: G 91 ASP cc_start: 0.8795 (t0) cc_final: 0.8454 (t70) REVERT: K 145 GLU cc_start: 0.8968 (tt0) cc_final: 0.8747 (tm-30) outliers start: 20 outliers final: 16 residues processed: 184 average time/residue: 0.2697 time to fit residues: 69.7186 Evaluate side-chains 190 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.095139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056685 restraints weight = 37559.621| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.32 r_work: 0.2723 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13842 Z= 0.320 Angle : 0.655 13.169 19832 Z= 0.377 Chirality : 0.038 0.163 2240 Planarity : 0.004 0.038 1530 Dihedral : 29.186 169.603 4128 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.77 % Allowed : 12.55 % Favored : 84.68 % 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: 2.77 (0.28), residues: 883 helix: 2.58 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.63 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 51 HIS 0.004 0.001 HIS D 110 PHE 0.038 0.002 PHE K 187 TYR 0.016 0.002 TYR H 84 ARG 0.010 0.001 ARG K 201 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 850) hydrogen bonds : angle 3.45467 ( 2171) covalent geometry : bond 0.00737 (13824) covalent geometry : angle 0.65504 (19832) Misc. bond : bond 0.00021 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.977 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: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8773 (m) cc_final: 0.8205 (t) REVERT: A 60 GLU cc_start: 0.8492 (pm20) cc_final: 0.7448 (pm20) REVERT: C 92 GLU cc_start: 0.8709 (pm20) cc_final: 0.8456 (pm20) REVERT: D 94 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: D 102 LEU cc_start: 0.9558 (mm) cc_final: 0.9314 (mm) REVERT: E 60 GLU cc_start: 0.8520 (pm20) cc_final: 0.8068 (pm20) REVERT: G 20 SER cc_start: 0.9668 (t) cc_final: 0.9299 (p) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.2574 time to fit residues: 63.0726 Evaluate side-chains 174 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.0050 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.097528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060174 restraints weight = 37585.026| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.28 r_work: 0.2812 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13842 Z= 0.168 Angle : 0.581 13.377 19832 Z= 0.339 Chirality : 0.033 0.148 2240 Planarity : 0.004 0.039 1530 Dihedral : 28.708 169.336 4128 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.98 % Allowed : 13.47 % Favored : 84.54 % 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: 3.01 (0.28), residues: 883 helix: 2.75 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.57 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 51 HIS 0.002 0.001 HIS F 76 PHE 0.038 0.002 PHE K 187 TYR 0.016 0.001 TYR H 84 ARG 0.007 0.000 ARG K 201 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 850) hydrogen bonds : angle 3.06357 ( 2171) covalent geometry : bond 0.00369 (13824) covalent geometry : angle 0.58115 (19832) Misc. bond : bond 0.00010 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8188 (t) REVERT: A 60 GLU cc_start: 0.8504 (pm20) cc_final: 0.7492 (pm20) REVERT: A 91 MET cc_start: 0.8850 (mmt) cc_final: 0.8643 (mmm) REVERT: C 39 ASN cc_start: 0.8742 (t0) cc_final: 0.8362 (t0) REVERT: C 92 GLU cc_start: 0.8725 (pm20) cc_final: 0.8486 (pm20) REVERT: D 94 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: D 102 LEU cc_start: 0.9495 (mm) cc_final: 0.9264 (mm) REVERT: D 109 LYS cc_start: 0.8668 (tttt) cc_final: 0.8448 (tttt) REVERT: E 60 GLU cc_start: 0.8467 (pm20) cc_final: 0.8012 (pm20) REVERT: G 20 SER cc_start: 0.9635 (t) cc_final: 0.9270 (p) REVERT: G 91 ASP cc_start: 0.8692 (t0) cc_final: 0.8329 (t70) REVERT: K 145 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8757 (pp20) outliers start: 15 outliers final: 11 residues processed: 178 average time/residue: 0.2648 time to fit residues: 66.6152 Evaluate side-chains 176 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2715 > 50: distance: 49 - 66: 27.264 distance: 54 - 74: 32.961 distance: 62 - 66: 29.773 distance: 66 - 67: 31.708 distance: 67 - 68: 30.676 distance: 67 - 70: 20.045 distance: 68 - 69: 13.979 distance: 68 - 74: 35.984 distance: 70 - 71: 27.659 distance: 71 - 72: 15.235 distance: 71 - 73: 3.442 distance: 74 - 75: 14.244 distance: 75 - 76: 17.715 distance: 75 - 78: 10.075 distance: 76 - 82: 14.268 distance: 78 - 79: 11.588 distance: 79 - 81: 38.347 distance: 82 - 83: 33.538 distance: 82 - 88: 18.088 distance: 83 - 84: 4.046 distance: 83 - 86: 9.572 distance: 84 - 85: 25.062 distance: 84 - 89: 7.421 distance: 85 - 110: 23.932 distance: 86 - 87: 9.843 distance: 87 - 88: 16.940 distance: 89 - 90: 3.884 distance: 90 - 91: 21.332 distance: 91 - 92: 20.685 distance: 91 - 93: 10.250 distance: 92 - 115: 19.220 distance: 93 - 94: 12.874 distance: 94 - 95: 8.475 distance: 94 - 97: 42.946 distance: 95 - 96: 31.316 distance: 95 - 102: 30.906 distance: 97 - 98: 12.759 distance: 98 - 99: 38.981 distance: 102 - 103: 27.681 distance: 103 - 104: 46.276 distance: 103 - 106: 11.687 distance: 104 - 105: 17.004 distance: 104 - 110: 43.291 distance: 105 - 134: 45.373 distance: 107 - 108: 7.816 distance: 110 - 111: 38.340 distance: 111 - 112: 5.281 distance: 111 - 114: 16.052 distance: 112 - 113: 18.368 distance: 112 - 115: 15.981 distance: 113 - 139: 28.573 distance: 115 - 116: 27.807 distance: 116 - 117: 3.870 distance: 117 - 118: 27.585 distance: 117 - 124: 40.773 distance: 118 - 146: 21.784 distance: 120 - 121: 22.233 distance: 121 - 122: 33.629 distance: 124 - 125: 8.409 distance: 125 - 126: 10.227 distance: 125 - 128: 24.121 distance: 126 - 127: 8.340 distance: 126 - 134: 41.461 distance: 127 - 152: 31.688 distance: 128 - 129: 14.491 distance: 129 - 130: 15.286 distance: 129 - 131: 14.898 distance: 130 - 132: 3.507 distance: 132 - 133: 3.670 distance: 134 - 135: 29.743 distance: 135 - 136: 42.153 distance: 135 - 138: 27.743 distance: 136 - 137: 16.308 distance: 136 - 139: 24.768 distance: 137 - 159: 30.788