Starting phenix.real_space_refine on Fri Sep 19 01:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipu_60781/09_2025/9ipu_60781.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8091 atoms to isotropic. 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 Zn 2 6.06 5 P 340 5.49 5 S 30 5.16 5 C 8838 2.51 5 N 2924 2.21 5 O 3616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15750 Number of models: 1 Model: "" Number of chains: 15 Chain: "I" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 526 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1125 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 407 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 55} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3488 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "N" Number of atoms: 3484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3484 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7931 SG CYS L 31 64.159 100.830 26.967 1.00218.04 S ATOM 8073 SG CYS L 51 66.529 103.652 27.672 1.00210.14 S ATOM 8097 SG CYS L 54 63.002 104.560 26.813 1.00213.50 S ATOM 7822 SG CYS L 16 75.394 98.933 21.484 1.00283.03 S ATOM 7840 SG CYS L 19 78.982 98.250 20.552 1.00282.47 S ATOM 7970 SG CYS L 36 77.356 96.060 23.117 1.00253.66 S ATOM 7988 SG CYS L 39 78.088 99.560 24.108 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 3.84, per 1000 atoms: 0.24 Number of scatterers: 15750 At special positions: 0 Unit cell: (124.584, 155.73, 110.622, 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) Zn 2 29.99 S 30 16.00 P 340 15.00 O 3616 8.00 N 2924 7.00 C 8838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 501.7 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " Number of angles added : 9 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 62.1% alpha, 4.7% beta 148 base pairs and 314 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'I' and resid 27 through 39 Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 63 through 78 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.815A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.512A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.627A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 3.667A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.548A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.523A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.515A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.587A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.549A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 36 through 47 removed outlier: 4.833A pdb=" N GLU L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 69 removed outlier: 3.758A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 84 Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'I' and resid 45 through 46 removed outlier: 6.431A pdb=" N SER I 92 " --> pdb=" O THR I 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.469A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.816A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.062A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.292A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 38 Processing sheet with id=AB4, first strand: chain 'L' and resid 27 through 28 removed outlier: 3.552A pdb=" N LEU L 35 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 6 518 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 378 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 314 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3445 1.33 - 1.45: 5035 1.45 - 1.57: 7533 1.57 - 1.69: 677 1.69 - 1.81: 47 Bond restraints: 16737 Sorted by residual: bond pdb=" C1' DC J 75 " pdb=" N1 DC J 75 " ideal model delta sigma weight residual 1.490 1.391 0.099 3.00e-02 1.11e+03 1.09e+01 bond pdb=" C3' DA N -77 " pdb=" O3' DA N -77 " ideal model delta sigma weight residual 1.422 1.513 -0.091 3.00e-02 1.11e+03 9.14e+00 bond pdb=" C3' DT N -78 " pdb=" O3' DT N -78 " ideal model delta sigma weight residual 1.422 1.511 -0.089 3.00e-02 1.11e+03 8.89e+00 bond pdb=" O5' DG J 79 " pdb=" C5' DG J 79 " ideal model delta sigma weight residual 1.423 1.505 -0.082 3.00e-02 1.11e+03 7.50e+00 bond pdb=" P DT J 77 " pdb=" OP1 DT J 77 " ideal model delta sigma weight residual 1.480 1.534 -0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 22623 2.29 - 4.57: 1354 4.57 - 6.86: 102 6.86 - 9.14: 26 9.14 - 11.43: 2 Bond angle restraints: 24107 Sorted by residual: angle pdb=" C3' DT N 54 " pdb=" O3' DT N 54 " pdb=" P DC N 55 " ideal model delta sigma weight residual 120.20 129.30 -9.10 1.50e+00 4.44e-01 3.68e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 128.82 -8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C3' DG J -58 " pdb=" O3' DG J -58 " pdb=" P DC J -57 " ideal model delta sigma weight residual 120.20 128.79 -8.59 1.50e+00 4.44e-01 3.28e+01 angle pdb=" C4' DA J -54 " pdb=" C3' DA J -54 " pdb=" O3' DA J -54 " ideal model delta sigma weight residual 110.00 101.76 8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 128.35 -8.15 1.50e+00 4.44e-01 2.95e+01 ... (remaining 24102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 7230 31.37 - 62.74: 1890 62.74 - 94.11: 52 94.11 - 125.48: 10 125.48 - 156.85: 3 Dihedral angle restraints: 9185 sinusoidal: 5901 harmonic: 3284 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 63.15 156.85 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT N 54 " pdb=" C3' DT N 54 " pdb=" O3' DT N 54 " pdb=" P DC N 55 " ideal model delta sinusoidal sigma weight residual 220.00 70.75 149.25 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 92.31 127.69 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2636 0.118 - 0.236: 114 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C1' DC J 75 " pdb=" O4' DC J 75 " pdb=" C2' DC J 75 " pdb=" N1 DC J 75 " both_signs ideal model delta sigma weight residual False 2.47 1.88 0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" C1' DG N -76 " pdb=" O4' DG N -76 " pdb=" C2' DG N -76 " pdb=" N9 DG N -76 " both_signs ideal model delta sigma weight residual False 2.42 2.14 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DT N 54 " pdb=" C4' DT N 54 " pdb=" O3' DT N 54 " pdb=" C2' DT N 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2750 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 93 " 0.051 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE I 93 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 93 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE I 93 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE I 93 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 93 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 93 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N -77 " 0.045 2.00e-02 2.50e+03 2.43e-02 1.62e+01 pdb=" N9 DA N -77 " -0.062 2.00e-02 2.50e+03 pdb=" C8 DA N -77 " 0.018 2.00e-02 2.50e+03 pdb=" N7 DA N -77 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA N -77 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA N -77 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA N -77 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA N -77 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DA N -77 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA N -77 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA N -77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -76 " 0.027 2.00e-02 2.50e+03 1.69e-02 8.59e+00 pdb=" N9 DG N -76 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG N -76 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG N -76 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG N -76 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DG N -76 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG N -76 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG N -76 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG N -76 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG N -76 " 0.000 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 49 2.43 - 3.05: 9017 3.05 - 3.66: 25654 3.66 - 4.28: 40993 4.28 - 4.90: 60451 Nonbonded interactions: 136164 Sorted by model distance: nonbonded pdb=" NH1 ARG E 49 " pdb=" C5' DA N -66 " model vdw 1.810 3.520 nonbonded pdb=" CG2 THR A 45 " pdb=" OP1 DG N 70 " model vdw 1.933 3.460 nonbonded pdb=" NH1 ARG A 49 " pdb=" C5' DA J -66 " model vdw 2.017 3.520 nonbonded pdb=" NH1 ARG I 74 " pdb=" OP1 DC N 80 " model vdw 2.072 3.120 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG N 48 " model vdw 2.073 3.040 ... (remaining 136159 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'J' and (resid -82 through -1 or resid 1 through 83)) selection = (chain 'N' and (resid -82 through -1 or resid 1 through 83)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.730 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 16745 Z= 0.316 Angle : 1.110 11.426 24116 Z= 0.690 Chirality : 0.056 0.590 2753 Planarity : 0.005 0.092 1880 Dihedral : 27.547 156.849 7057 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.63 % Allowed : 4.35 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.26), residues: 1100 helix: 1.86 (0.20), residues: 698 sheet: -0.65 (0.85), residues: 33 loop : -0.68 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 47 TYR 0.031 0.002 TYR I 28 PHE 0.051 0.002 PHE I 93 TRP 0.011 0.002 TRP K 93 HIS 0.009 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00694 (16737) covalent geometry : angle 1.10891 (24107) hydrogen bonds : bond 0.16237 ( 896) hydrogen bonds : angle 6.08603 ( 2286) metal coordination : bond 0.00516 ( 8) metal coordination : angle 2.99243 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.506 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8250 (mt) cc_final: 0.7654 (mt) REVERT: A 106 ASP cc_start: 0.8636 (m-30) cc_final: 0.7923 (m-30) REVERT: E 120 MET cc_start: 0.7600 (ptp) cc_final: 0.7032 (ptm) REVERT: G 64 GLU cc_start: 0.9006 (tt0) cc_final: 0.8759 (tp30) REVERT: K 112 ASP cc_start: 0.9285 (t0) cc_final: 0.8934 (p0) REVERT: K 132 ASP cc_start: 0.9655 (t70) cc_final: 0.9432 (p0) REVERT: M 1 MET cc_start: 0.2658 (ptt) cc_final: 0.2387 (ptt) outliers start: 15 outliers final: 2 residues processed: 218 average time/residue: 0.1921 time to fit residues: 55.8746 Evaluate side-chains 93 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.039278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.027644 restraints weight = 238775.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.028284 restraints weight = 131114.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028628 restraints weight = 89112.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028898 restraints weight = 70983.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.029001 restraints weight = 61317.237| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16745 Z= 0.245 Angle : 0.717 8.986 24116 Z= 0.418 Chirality : 0.041 0.173 2753 Planarity : 0.005 0.060 1880 Dihedral : 31.179 151.588 4954 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1100 helix: 1.93 (0.20), residues: 695 sheet: -0.40 (0.85), residues: 33 loop : -0.67 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 92 TYR 0.016 0.001 TYR E 54 PHE 0.012 0.001 PHE E 104 TRP 0.010 0.002 TRP L 61 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00536 (16737) covalent geometry : angle 0.71598 (24107) hydrogen bonds : bond 0.07020 ( 896) hydrogen bonds : angle 3.59602 ( 2286) metal coordination : bond 0.00565 ( 8) metal coordination : angle 2.45931 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.436 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: 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 90 MET cc_start: 0.9192 (mmp) cc_final: 0.8803 (mmp) REVERT: A 106 ASP cc_start: 0.9286 (m-30) cc_final: 0.8834 (m-30) REVERT: B 49 LEU cc_start: 0.9631 (tt) cc_final: 0.9099 (tp) REVERT: B 59 LYS cc_start: 0.9615 (tttp) cc_final: 0.9315 (tptp) REVERT: B 63 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9251 (mt-10) REVERT: C 25 PHE cc_start: 0.9254 (m-80) cc_final: 0.8846 (m-10) REVERT: E 106 ASP cc_start: 0.9367 (m-30) cc_final: 0.8795 (m-30) REVERT: H 62 MET cc_start: 0.9652 (mmp) cc_final: 0.9305 (mmm) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.1793 time to fit residues: 32.6795 Evaluate side-chains 72 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** H 84 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 = 0.3163 r_free = 0.3163 target = 0.037899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026295 restraints weight = 246850.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026865 restraints weight = 138082.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.027102 restraints weight = 94063.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027284 restraints weight = 77791.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.027488 restraints weight = 68147.445| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16745 Z= 0.221 Angle : 0.665 8.059 24116 Z= 0.387 Chirality : 0.039 0.162 2753 Planarity : 0.005 0.050 1880 Dihedral : 31.272 161.177 4954 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.25), residues: 1100 helix: 1.70 (0.19), residues: 697 sheet: -0.37 (1.01), residues: 24 loop : -0.56 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 49 TYR 0.025 0.002 TYR L 64 PHE 0.018 0.001 PHE A 104 TRP 0.007 0.001 TRP K 93 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (16737) covalent geometry : angle 0.66367 (24107) hydrogen bonds : bond 0.05040 ( 896) hydrogen bonds : angle 3.54321 ( 2286) metal coordination : bond 0.00450 ( 8) metal coordination : angle 2.40077 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.415 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: 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 90 MET cc_start: 0.9197 (mmp) cc_final: 0.8851 (mmp) REVERT: A 106 ASP cc_start: 0.9257 (m-30) cc_final: 0.8748 (m-30) REVERT: B 49 LEU cc_start: 0.9444 (tt) cc_final: 0.9140 (tp) REVERT: B 59 LYS cc_start: 0.9618 (tttp) cc_final: 0.9337 (tptp) REVERT: B 63 GLU cc_start: 0.9619 (mt-10) cc_final: 0.9246 (mt-10) REVERT: C 25 PHE cc_start: 0.9307 (m-80) cc_final: 0.8877 (m-10) REVERT: D 59 MET cc_start: 0.9034 (tpp) cc_final: 0.8809 (tpp) REVERT: D 68 ASP cc_start: 0.9531 (t70) cc_final: 0.9303 (t0) REVERT: E 120 MET cc_start: 0.8569 (ptp) cc_final: 0.8241 (ptp) REVERT: G 64 GLU cc_start: 0.9791 (tt0) cc_final: 0.9496 (tm-30) REVERT: G 87 ILE cc_start: 0.9646 (mm) cc_final: 0.9340 (tp) REVERT: H 62 MET cc_start: 0.9648 (mmp) cc_final: 0.9318 (mmp) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.1639 time to fit residues: 26.2037 Evaluate side-chains 75 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS G 112 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024699 restraints weight = 255112.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025234 restraints weight = 147889.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025497 restraints weight = 104703.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.025612 restraints weight = 85688.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025824 restraints weight = 77311.234| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16745 Z= 0.263 Angle : 0.645 7.468 24116 Z= 0.378 Chirality : 0.038 0.176 2753 Planarity : 0.005 0.058 1880 Dihedral : 31.257 178.416 4954 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1100 helix: 1.68 (0.19), residues: 700 sheet: -0.40 (1.01), residues: 24 loop : -0.48 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 128 TYR 0.022 0.002 TYR I 58 PHE 0.012 0.002 PHE C 25 TRP 0.013 0.002 TRP L 77 HIS 0.014 0.002 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00571 (16737) covalent geometry : angle 0.64321 (24107) hydrogen bonds : bond 0.07102 ( 896) hydrogen bonds : angle 3.66179 ( 2286) metal coordination : bond 0.00598 ( 8) metal coordination : angle 2.27882 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.414 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9199 (mmp) cc_final: 0.8907 (mmp) REVERT: B 49 LEU cc_start: 0.9567 (tt) cc_final: 0.9145 (tt) REVERT: B 59 LYS cc_start: 0.9639 (tttp) cc_final: 0.9339 (tptp) REVERT: B 63 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9189 (mt-10) REVERT: D 59 MET cc_start: 0.9153 (tpp) cc_final: 0.8889 (tpp) REVERT: D 68 ASP cc_start: 0.9558 (t70) cc_final: 0.9334 (t0) REVERT: E 64 LYS cc_start: 0.9539 (mppt) cc_final: 0.9327 (mmtm) REVERT: E 120 MET cc_start: 0.8491 (ptp) cc_final: 0.8175 (ptp) REVERT: G 87 ILE cc_start: 0.9643 (mm) cc_final: 0.9351 (tp) REVERT: H 62 MET cc_start: 0.9644 (mmp) cc_final: 0.9317 (mmp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1662 time to fit residues: 22.7687 Evaluate side-chains 68 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 GLN D 109 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.037003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025582 restraints weight = 245123.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026044 restraints weight = 137154.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026508 restraints weight = 98319.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.026608 restraints weight = 76964.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.026608 restraints weight = 69876.413| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16745 Z= 0.167 Angle : 0.595 7.290 24116 Z= 0.346 Chirality : 0.036 0.167 2753 Planarity : 0.004 0.064 1880 Dihedral : 31.108 178.742 4954 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.25), residues: 1100 helix: 1.82 (0.19), residues: 702 sheet: -0.31 (1.00), residues: 24 loop : -0.52 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.023 0.001 TYR L 64 PHE 0.011 0.001 PHE C 25 TRP 0.006 0.001 TRP L 61 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (16737) covalent geometry : angle 0.59381 (24107) hydrogen bonds : bond 0.03661 ( 896) hydrogen bonds : angle 3.39431 ( 2286) metal coordination : bond 0.00400 ( 8) metal coordination : angle 1.87113 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.520 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9260 (mmp) cc_final: 0.8972 (mmp) REVERT: D 59 MET cc_start: 0.9090 (tpp) cc_final: 0.8788 (tpp) REVERT: D 68 ASP cc_start: 0.9522 (t70) cc_final: 0.9298 (t0) REVERT: D 71 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9185 (mt-10) REVERT: E 64 LYS cc_start: 0.9544 (mppt) cc_final: 0.9326 (mmtm) REVERT: E 106 ASP cc_start: 0.9426 (m-30) cc_final: 0.9096 (m-30) REVERT: E 120 MET cc_start: 0.8317 (ptp) cc_final: 0.8077 (ptp) REVERT: G 64 GLU cc_start: 0.9799 (tt0) cc_final: 0.9484 (tm-30) REVERT: G 87 ILE cc_start: 0.9612 (mm) cc_final: 0.9299 (tp) REVERT: G 104 GLN cc_start: 0.9457 (mm-40) cc_final: 0.9134 (mm-40) REVERT: H 59 MET cc_start: 0.9556 (tpt) cc_final: 0.9329 (tpt) REVERT: H 62 MET cc_start: 0.9626 (mmp) cc_final: 0.9297 (mmp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1625 time to fit residues: 23.7868 Evaluate side-chains 67 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.035131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.023898 restraints weight = 257975.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024368 restraints weight = 149474.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.024516 restraints weight = 108721.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024842 restraints weight = 94617.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024805 restraints weight = 83103.631| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16745 Z= 0.268 Angle : 0.632 7.362 24116 Z= 0.370 Chirality : 0.039 0.339 2753 Planarity : 0.005 0.055 1880 Dihedral : 31.106 179.925 4954 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1100 helix: 1.75 (0.19), residues: 700 sheet: -0.54 (0.99), residues: 24 loop : -0.67 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 88 TYR 0.012 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 TRP 0.007 0.001 TRP K 93 HIS 0.015 0.001 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00584 (16737) covalent geometry : angle 0.63029 (24107) hydrogen bonds : bond 0.07423 ( 896) hydrogen bonds : angle 3.64660 ( 2286) metal coordination : bond 0.00647 ( 8) metal coordination : angle 2.13271 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.363 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: symmetry clash REVERT: A 90 MET cc_start: 0.9247 (mmp) cc_final: 0.8976 (mmp) REVERT: A 120 MET cc_start: 0.8417 (mtm) cc_final: 0.7809 (mtt) REVERT: B 49 LEU cc_start: 0.9652 (tp) cc_final: 0.9291 (tt) REVERT: B 63 GLU cc_start: 0.9589 (mt-10) cc_final: 0.9345 (mt-10) REVERT: C 79 ILE cc_start: 0.9766 (tp) cc_final: 0.9564 (pt) REVERT: D 59 MET cc_start: 0.9123 (tpp) cc_final: 0.8841 (tpp) REVERT: D 68 ASP cc_start: 0.9542 (t70) cc_final: 0.9274 (t0) REVERT: E 120 MET cc_start: 0.8521 (ptp) cc_final: 0.8124 (ptp) REVERT: G 87 ILE cc_start: 0.9618 (mm) cc_final: 0.9316 (tp) REVERT: G 104 GLN cc_start: 0.9487 (mm-40) cc_final: 0.9152 (mm-40) REVERT: H 62 MET cc_start: 0.9620 (mmp) cc_final: 0.9312 (mmp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1553 time to fit residues: 20.0048 Evaluate side-chains 62 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 96 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.023653 restraints weight = 257679.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024121 restraints weight = 148943.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.024480 restraints weight = 106994.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024599 restraints weight = 87935.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024599 restraints weight = 78617.826| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16745 Z= 0.234 Angle : 0.630 7.322 24116 Z= 0.365 Chirality : 0.038 0.247 2753 Planarity : 0.005 0.058 1880 Dihedral : 31.248 179.239 4954 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1100 helix: 1.60 (0.19), residues: 704 sheet: -0.54 (0.99), residues: 24 loop : -0.60 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.021 0.002 TYR L 64 PHE 0.011 0.002 PHE A 104 TRP 0.014 0.002 TRP L 61 HIS 0.005 0.001 HIS L 65 Details of bonding type rmsd covalent geometry : bond 0.00503 (16737) covalent geometry : angle 0.62839 (24107) hydrogen bonds : bond 0.05481 ( 896) hydrogen bonds : angle 3.69399 ( 2286) metal coordination : bond 0.00666 ( 8) metal coordination : angle 2.31663 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.376 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 90 MET cc_start: 0.9245 (mmp) cc_final: 0.8978 (mmp) REVERT: A 120 MET cc_start: 0.8369 (mtm) cc_final: 0.7802 (mtt) REVERT: B 49 LEU cc_start: 0.9624 (tp) cc_final: 0.9247 (tt) REVERT: B 63 GLU cc_start: 0.9577 (mt-10) cc_final: 0.9287 (tp30) REVERT: D 37 TYR cc_start: 0.9423 (m-10) cc_final: 0.9200 (m-10) REVERT: D 59 MET cc_start: 0.9105 (tpp) cc_final: 0.8818 (tpp) REVERT: D 71 GLU cc_start: 0.9142 (mp0) cc_final: 0.8935 (mp0) REVERT: E 120 MET cc_start: 0.8373 (ptp) cc_final: 0.8089 (ptp) REVERT: G 61 GLU cc_start: 0.9538 (tp30) cc_final: 0.9229 (tp30) REVERT: G 64 GLU cc_start: 0.9815 (tt0) cc_final: 0.9405 (tm-30) REVERT: G 104 GLN cc_start: 0.9499 (mm-40) cc_final: 0.9161 (mm-40) REVERT: H 59 MET cc_start: 0.9517 (tpt) cc_final: 0.9258 (tpt) REVERT: H 62 MET cc_start: 0.9626 (mmp) cc_final: 0.9298 (mmp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1558 time to fit residues: 19.9823 Evaluate side-chains 61 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- 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 = 0.3051 r_free = 0.3051 target = 0.034517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.023413 restraints weight = 260817.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.023816 restraints weight = 150130.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023981 restraints weight = 108167.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.024016 restraints weight = 95817.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024366 restraints weight = 93579.532| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16745 Z= 0.226 Angle : 0.616 7.278 24116 Z= 0.357 Chirality : 0.037 0.206 2753 Planarity : 0.005 0.059 1880 Dihedral : 31.152 179.458 4954 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1100 helix: 1.60 (0.19), residues: 707 sheet: -0.48 (1.00), residues: 24 loop : -0.66 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 99 TYR 0.019 0.001 TYR L 64 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP K 93 HIS 0.004 0.001 HIS L 65 Details of bonding type rmsd covalent geometry : bond 0.00495 (16737) covalent geometry : angle 0.61466 (24107) hydrogen bonds : bond 0.05942 ( 896) hydrogen bonds : angle 3.66142 ( 2286) metal coordination : bond 0.00631 ( 8) metal coordination : angle 2.14429 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.447 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 90 MET cc_start: 0.9261 (mmp) cc_final: 0.8992 (mmp) REVERT: B 49 LEU cc_start: 0.9693 (tp) cc_final: 0.9198 (tt) REVERT: B 58 LEU cc_start: 0.9924 (tp) cc_final: 0.9606 (pp) REVERT: D 37 TYR cc_start: 0.9410 (m-10) cc_final: 0.9113 (m-10) REVERT: D 59 MET cc_start: 0.9105 (tpp) cc_final: 0.8810 (tpp) REVERT: D 68 ASP cc_start: 0.9554 (t70) cc_final: 0.9338 (t0) REVERT: E 120 MET cc_start: 0.8223 (ptp) cc_final: 0.7977 (ptp) REVERT: G 61 GLU cc_start: 0.9521 (tp30) cc_final: 0.9207 (tp30) REVERT: G 64 GLU cc_start: 0.9803 (tt0) cc_final: 0.9398 (tm-30) REVERT: G 87 ILE cc_start: 0.9597 (mm) cc_final: 0.9287 (tp) REVERT: G 104 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9115 (mm-40) REVERT: H 62 MET cc_start: 0.9634 (mmp) cc_final: 0.9299 (mmp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1563 time to fit residues: 19.8757 Evaluate side-chains 64 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022508 restraints weight = 266701.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.022904 restraints weight = 157412.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.023049 restraints weight = 117089.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023368 restraints weight = 101444.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.023469 restraints weight = 87993.664| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16745 Z= 0.282 Angle : 0.651 7.312 24116 Z= 0.378 Chirality : 0.039 0.183 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.385 179.126 4954 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1100 helix: 1.43 (0.19), residues: 704 sheet: -0.70 (1.00), residues: 24 loop : -0.73 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 99 TYR 0.021 0.002 TYR F 72 PHE 0.027 0.002 PHE A 104 TRP 0.010 0.002 TRP L 77 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00611 (16737) covalent geometry : angle 0.65001 (24107) hydrogen bonds : bond 0.07463 ( 896) hydrogen bonds : angle 3.85147 ( 2286) metal coordination : bond 0.00946 ( 8) metal coordination : angle 2.33707 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.482 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 74 ILE cc_start: 0.9769 (tp) cc_final: 0.9561 (tp) REVERT: A 90 MET cc_start: 0.9228 (mmp) cc_final: 0.8960 (mmp) REVERT: A 120 MET cc_start: 0.8304 (mtm) cc_final: 0.7668 (mtp) REVERT: B 49 LEU cc_start: 0.9614 (tp) cc_final: 0.9207 (tt) REVERT: B 58 LEU cc_start: 0.9919 (tp) cc_final: 0.9613 (pp) REVERT: D 37 TYR cc_start: 0.9467 (m-10) cc_final: 0.9136 (m-10) REVERT: D 59 MET cc_start: 0.9112 (tpp) cc_final: 0.8820 (tpp) REVERT: D 68 ASP cc_start: 0.9571 (t70) cc_final: 0.9339 (t0) REVERT: D 71 GLU cc_start: 0.9383 (mp0) cc_final: 0.9083 (mp0) REVERT: E 120 MET cc_start: 0.8197 (ptp) cc_final: 0.7969 (ptp) REVERT: G 64 GLU cc_start: 0.9777 (tt0) cc_final: 0.9263 (tp30) REVERT: G 104 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9087 (mm-40) REVERT: H 59 MET cc_start: 0.9503 (tpt) cc_final: 0.9290 (tpt) REVERT: H 62 MET cc_start: 0.9597 (mmp) cc_final: 0.9274 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1578 time to fit residues: 19.5483 Evaluate side-chains 59 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 90 optimal weight: 0.0270 chunk 121 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS D 109 HIS ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.034042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.023051 restraints weight = 261743.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.023483 restraints weight = 150666.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.023651 restraints weight = 109188.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.023944 restraints weight = 93511.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.024028 restraints weight = 81572.622| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16745 Z= 0.208 Angle : 0.621 7.466 24116 Z= 0.360 Chirality : 0.038 0.184 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.321 179.414 4954 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1100 helix: 1.52 (0.19), residues: 704 sheet: -0.54 (0.97), residues: 24 loop : -0.75 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 99 TYR 0.033 0.002 TYR L 64 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.002 TRP L 77 HIS 0.006 0.001 HIS L 65 Details of bonding type rmsd covalent geometry : bond 0.00452 (16737) covalent geometry : angle 0.61988 (24107) hydrogen bonds : bond 0.05272 ( 896) hydrogen bonds : angle 3.72508 ( 2286) metal coordination : bond 0.00745 ( 8) metal coordination : angle 2.04414 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.476 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 90 MET cc_start: 0.9285 (mmp) cc_final: 0.9023 (mmp) REVERT: B 58 LEU cc_start: 0.9898 (tp) cc_final: 0.9580 (pp) REVERT: D 37 TYR cc_start: 0.9451 (m-10) cc_final: 0.9013 (m-10) REVERT: D 59 MET cc_start: 0.9088 (tpp) cc_final: 0.8795 (tpp) REVERT: D 68 ASP cc_start: 0.9577 (t70) cc_final: 0.9304 (t0) REVERT: D 71 GLU cc_start: 0.9370 (mp0) cc_final: 0.9068 (mp0) REVERT: E 120 MET cc_start: 0.8138 (ptp) cc_final: 0.7925 (ptp) REVERT: G 64 GLU cc_start: 0.9736 (tt0) cc_final: 0.9417 (tm-30) REVERT: G 104 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9059 (mm-40) REVERT: H 59 MET cc_start: 0.9574 (tpt) cc_final: 0.8678 (tpt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1498 time to fit residues: 19.2652 Evaluate side-chains 66 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 50.0000 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.033126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.022937 restraints weight = 264642.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.023019 restraints weight = 161957.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.023240 restraints weight = 111610.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.023435 restraints weight = 91372.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.023453 restraints weight = 80103.489| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16745 Z= 0.271 Angle : 0.650 9.947 24116 Z= 0.375 Chirality : 0.039 0.202 2753 Planarity : 0.005 0.061 1880 Dihedral : 31.332 178.559 4954 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1100 helix: 1.34 (0.19), residues: 704 sheet: -0.22 (0.87), residues: 33 loop : -0.87 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 99 TYR 0.015 0.002 TYR D 37 PHE 0.012 0.002 PHE I 93 TRP 0.009 0.002 TRP K 93 HIS 0.005 0.001 HIS L 65 Details of bonding type rmsd covalent geometry : bond 0.00589 (16737) covalent geometry : angle 0.64862 (24107) hydrogen bonds : bond 0.07579 ( 896) hydrogen bonds : angle 3.85263 ( 2286) metal coordination : bond 0.00983 ( 8) metal coordination : angle 2.19056 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.05 seconds wall clock time: 47 minutes 34.44 seconds (2854.44 seconds total)