Starting phenix.real_space_refine on Wed Jul 30 23:44:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.048 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnv_17786/07_2025/8pnv_17786.cif" } resolution = 2.048 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 60 5.16 5 C 8202 2.51 5 N 2106 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13098 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: D, F, K, J, L, C, B, G, I, H Time building chain proxies: 6.39, per 1000 atoms: 0.49 Number of scatterers: 13098 At special positions: 0 Unit cell: (79.2, 81.18, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 60 16.00 O 2724 8.00 N 2106 7.00 C 8202 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 24 sheets defined 47.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 155 Proline residue: A 134 - end of helix removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Proline residue: B 61 - end of helix Processing helix chain 'B' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 155 Proline residue: B 134 - end of helix removed outlier: 3.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 Proline residue: C 61 - end of helix Processing helix chain 'C' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 155 Proline residue: C 134 - end of helix removed outlier: 3.654A pdb=" N LEU C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 75 Proline residue: G 61 - end of helix Processing helix chain 'G' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY G 79 " --> pdb=" O PRO G 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 79' Processing helix chain 'G' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN G 107 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 155 Proline residue: G 134 - end of helix removed outlier: 3.654A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 75 Proline residue: H 61 - end of helix Processing helix chain 'H' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 79' Processing helix chain 'H' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN H 107 " --> pdb=" O TYR H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 155 Proline residue: H 134 - end of helix removed outlier: 3.654A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 75 Proline residue: I 61 - end of helix Processing helix chain 'I' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY I 79 " --> pdb=" O PRO I 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN I 107 " --> pdb=" O TYR I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 155 Proline residue: I 134 - end of helix removed outlier: 3.655A pdb=" N LEU I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'K' and resid 63 through 66 Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'L' and resid 63 through 66 Processing helix chain 'L' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU A 36 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 43 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 38 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU B 36 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 43 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 38 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU C 36 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 43 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 38 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL D 35 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL E 35 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR E 51 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL F 35 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR F 51 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'G' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU G 36 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE G 43 " --> pdb=" O GLU G 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 38 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU H 36 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE H 43 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE H 38 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU I 36 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE I 43 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE I 38 " --> pdb=" O TYR I 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL J 35 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR J 51 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AC1, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL K 35 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP K 37 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 12 through 14 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL L 35 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR L 51 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 14 810 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5428 1.39 - 1.55: 7412 1.55 - 1.72: 0 1.72 - 1.88: 102 1.88 - 2.05: 24 Bond restraints: 12966 Sorted by residual: bond pdb=" CB ASN L 53 " pdb=" CG ASN L 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.58e+00 bond pdb=" CB ASN F 53 " pdb=" CG ASN F 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.55e+00 bond pdb=" CB ASN K 53 " pdb=" CG ASN K 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CB ASN E 53 " pdb=" CG ASN E 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.48e+00 bond pdb=" CB ASN D 53 " pdb=" CG ASN D 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.44e+00 ... (remaining 12961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17009 1.39 - 2.78: 495 2.78 - 4.17: 112 4.17 - 5.56: 36 5.56 - 6.95: 18 Bond angle restraints: 17670 Sorted by residual: angle pdb=" C ILE J 52 " pdb=" N ASN J 53 " pdb=" CA ASN J 53 " ideal model delta sigma weight residual 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.37e+01 angle pdb=" C ILE D 52 " pdb=" N ASN D 53 " pdb=" CA ASN D 53 " ideal model delta sigma weight residual 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.36e+01 angle pdb=" C ILE K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.06 127.96 -6.90 1.88e+00 2.83e-01 1.35e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 6192 17.03 - 34.07: 756 34.07 - 51.10: 138 51.10 - 68.14: 108 68.14 - 85.17: 30 Dihedral angle restraints: 7224 sinusoidal: 2754 harmonic: 4470 Sorted by residual: dihedral pdb=" CA ASP L 74 " pdb=" CB ASP L 74 " pdb=" CG ASP L 74 " pdb=" OD1 ASP L 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP F 74 " pdb=" CB ASP F 74 " pdb=" CG ASP F 74 " pdb=" OD1 ASP F 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP J 74 " pdb=" CB ASP J 74 " pdb=" CG ASP J 74 " pdb=" OD1 ASP J 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 7221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1075 0.030 - 0.059: 444 0.059 - 0.089: 200 0.089 - 0.119: 84 0.119 - 0.148: 21 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ILE H 43 " pdb=" N ILE H 43 " pdb=" C ILE H 43 " pdb=" CB ILE H 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE G 43 " pdb=" N ILE G 43 " pdb=" C ILE G 43 " pdb=" CB ILE G 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1821 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 63 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO L 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 63 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 64 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 63 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO E 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.037 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 210 2.61 - 3.18: 11100 3.18 - 3.76: 22159 3.76 - 4.33: 30704 4.33 - 4.90: 49905 Nonbonded interactions: 114078 Sorted by model distance: nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 97 " model vdw 2.040 3.760 ... (remaining 114073 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: 0.10 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'G' selection = chain 'I' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12972 Z= 0.187 Angle : 0.662 6.948 17670 Z= 0.340 Chirality : 0.043 0.148 1824 Planarity : 0.006 0.067 2244 Dihedral : 17.458 85.170 4428 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.87 % Allowed : 19.62 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.20), residues: 1602 helix: 3.28 (0.19), residues: 678 sheet: 0.89 (0.31), residues: 228 loop : 0.43 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 28 HIS 0.002 0.001 HIS I 12 PHE 0.016 0.002 PHE L 48 TYR 0.013 0.002 TYR A 103 ARG 0.003 0.000 ARG G 112 Details of bonding type rmsd hydrogen bonds : bond 0.11184 ( 774) hydrogen bonds : angle 5.22320 ( 2196) covalent geometry : bond 0.00397 (12966) covalent geometry : angle 0.66177 (17670) Misc. bond : bond 0.00155 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: F 107 GLU cc_start: 0.6856 (tt0) cc_final: 0.6574 (tt0) REVERT: J 107 GLU cc_start: 0.6895 (tt0) cc_final: 0.6589 (tt0) outliers start: 36 outliers final: 32 residues processed: 296 average time/residue: 1.2318 time to fit residues: 398.1168 Evaluate side-chains 286 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 118 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN C 30 ASN D 86 ASN G 30 ASN I 30 ASN K 86 ASN L 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116401 restraints weight = 10554.488| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.93 r_work: 0.3171 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12972 Z= 0.286 Angle : 0.783 8.534 17670 Z= 0.414 Chirality : 0.048 0.152 1824 Planarity : 0.006 0.045 2244 Dihedral : 10.607 84.237 1850 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.58 % Allowed : 14.83 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 1602 helix: 2.81 (0.19), residues: 678 sheet: 0.51 (0.31), residues: 228 loop : 0.07 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP F 54 HIS 0.004 0.002 HIS H 12 PHE 0.019 0.003 PHE K 48 TYR 0.019 0.004 TYR I 103 ARG 0.006 0.001 ARG L 28 Details of bonding type rmsd hydrogen bonds : bond 0.09659 ( 774) hydrogen bonds : angle 5.22854 ( 2196) covalent geometry : bond 0.00616 (12966) covalent geometry : angle 0.78327 (17670) Misc. bond : bond 0.02613 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7376 (mtt-85) REVERT: B 86 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7426 (mtt-85) REVERT: E 93 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7276 (p0) REVERT: F 93 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7269 (p0) REVERT: H 86 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (mtt-85) REVERT: I 86 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7383 (mtt-85) REVERT: J 93 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7293 (p0) REVERT: L 93 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7291 (p0) outliers start: 70 outliers final: 44 residues processed: 300 average time/residue: 1.2615 time to fit residues: 412.6436 Evaluate side-chains 295 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 118 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120037 restraints weight = 10770.372| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.95 r_work: 0.3217 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12972 Z= 0.162 Angle : 0.605 5.957 17670 Z= 0.308 Chirality : 0.042 0.132 1824 Planarity : 0.004 0.032 2244 Dihedral : 9.397 79.505 1848 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 16.11 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.20), residues: 1602 helix: 3.30 (0.19), residues: 678 sheet: 0.50 (0.29), residues: 228 loop : 0.02 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 54 HIS 0.002 0.000 HIS F 58 PHE 0.017 0.001 PHE D 48 TYR 0.008 0.002 TYR K 96 ARG 0.002 0.000 ARG H 112 Details of bonding type rmsd hydrogen bonds : bond 0.07273 ( 774) hydrogen bonds : angle 4.75191 ( 2196) covalent geometry : bond 0.00343 (12966) covalent geometry : angle 0.60506 (17670) Misc. bond : bond 0.02360 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7255 (mtt-85) REVERT: D 93 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (p0) REVERT: F 107 GLU cc_start: 0.7141 (tt0) cc_final: 0.6934 (tt0) REVERT: K 93 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7367 (p0) outliers start: 38 outliers final: 18 residues processed: 271 average time/residue: 1.2749 time to fit residues: 376.5929 Evaluate side-chains 261 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 112 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122342 restraints weight = 10760.100| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 0.94 r_work: 0.3249 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12972 Z= 0.145 Angle : 0.574 6.717 17670 Z= 0.288 Chirality : 0.041 0.130 1824 Planarity : 0.004 0.029 2244 Dihedral : 8.493 78.772 1807 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.87 % Allowed : 16.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.20), residues: 1602 helix: 3.48 (0.18), residues: 678 sheet: 0.49 (0.28), residues: 228 loop : 0.09 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 54 HIS 0.001 0.000 HIS F 58 PHE 0.017 0.001 PHE D 48 TYR 0.007 0.001 TYR K 108 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.06482 ( 774) hydrogen bonds : angle 4.54134 ( 2196) covalent geometry : bond 0.00314 (12966) covalent geometry : angle 0.57402 (17670) Misc. bond : bond 0.02001 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 82 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5533 (t0) REVERT: D 93 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7322 (p0) REVERT: E 93 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7132 (p0) REVERT: F 93 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7115 (p0) REVERT: H 82 ASP cc_start: 0.5856 (OUTLIER) cc_final: 0.5524 (t0) REVERT: J 93 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7127 (p0) REVERT: K 93 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7317 (p0) REVERT: L 93 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7128 (p0) outliers start: 36 outliers final: 17 residues processed: 260 average time/residue: 1.2695 time to fit residues: 360.2347 Evaluate side-chains 255 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120686 restraints weight = 10778.871| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.95 r_work: 0.3228 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12972 Z= 0.156 Angle : 0.592 6.011 17670 Z= 0.298 Chirality : 0.041 0.129 1824 Planarity : 0.004 0.029 2244 Dihedral : 8.512 79.533 1806 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.59 % Allowed : 15.15 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1602 helix: 3.42 (0.18), residues: 678 sheet: 0.38 (0.28), residues: 234 loop : 0.06 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.001 0.000 HIS I 58 PHE 0.017 0.001 PHE D 48 TYR 0.008 0.002 TYR K 108 ARG 0.002 0.000 ARG H 112 Details of bonding type rmsd hydrogen bonds : bond 0.07003 ( 774) hydrogen bonds : angle 4.66258 ( 2196) covalent geometry : bond 0.00333 (12966) covalent geometry : angle 0.59219 (17670) Misc. bond : bond 0.02186 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 1.395 Fit side-chains REVERT: D 93 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7357 (p0) REVERT: E 93 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7136 (p0) REVERT: F 93 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7154 (p0) REVERT: J 93 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7162 (p0) REVERT: K 93 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7355 (p0) REVERT: L 93 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7136 (p0) outliers start: 45 outliers final: 27 residues processed: 268 average time/residue: 1.1912 time to fit residues: 349.5057 Evaluate side-chains 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119037 restraints weight = 10942.866| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.93 r_work: 0.3210 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12972 Z= 0.192 Angle : 0.651 5.923 17670 Z= 0.333 Chirality : 0.043 0.136 1824 Planarity : 0.004 0.035 2244 Dihedral : 8.574 81.123 1802 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.67 % Allowed : 15.15 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.20), residues: 1602 helix: 3.20 (0.19), residues: 678 sheet: 0.39 (0.28), residues: 234 loop : -0.07 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.002 0.001 HIS I 58 PHE 0.017 0.002 PHE D 48 TYR 0.011 0.002 TYR J 108 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.08094 ( 774) hydrogen bonds : angle 4.89366 ( 2196) covalent geometry : bond 0.00405 (12966) covalent geometry : angle 0.65059 (17670) Misc. bond : bond 0.02618 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.490 Fit side-chains REVERT: D 93 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7422 (p0) REVERT: E 93 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7189 (p0) REVERT: F 93 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7177 (p0) REVERT: G 156 SER cc_start: 0.4638 (OUTLIER) cc_final: 0.4430 (m) REVERT: I 156 SER cc_start: 0.4652 (OUTLIER) cc_final: 0.4390 (m) REVERT: J 93 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7182 (p0) REVERT: K 93 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7404 (p0) REVERT: L 93 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7197 (p0) outliers start: 46 outliers final: 31 residues processed: 266 average time/residue: 1.2274 time to fit residues: 356.3844 Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120995 restraints weight = 10842.725| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 0.94 r_work: 0.3239 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12972 Z= 0.160 Angle : 0.605 6.000 17670 Z= 0.305 Chirality : 0.042 0.132 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.399 79.646 1802 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.11 % Allowed : 15.15 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1602 helix: 3.34 (0.18), residues: 678 sheet: 0.42 (0.28), residues: 234 loop : -0.06 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 54 HIS 0.001 0.000 HIS F 58 PHE 0.017 0.002 PHE D 48 TYR 0.008 0.002 TYR K 108 ARG 0.002 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.07118 ( 774) hydrogen bonds : angle 4.69703 ( 2196) covalent geometry : bond 0.00343 (12966) covalent geometry : angle 0.60460 (17670) Misc. bond : bond 0.02129 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 156 SER cc_start: 0.4828 (OUTLIER) cc_final: 0.4518 (m) REVERT: C 156 SER cc_start: 0.4634 (OUTLIER) cc_final: 0.4411 (m) REVERT: D 93 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7380 (p0) REVERT: E 93 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7184 (p0) REVERT: F 20 ARG cc_start: 0.7976 (ttt-90) cc_final: 0.7363 (ttt180) REVERT: F 93 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7173 (p0) REVERT: G 156 SER cc_start: 0.4726 (OUTLIER) cc_final: 0.4482 (m) REVERT: H 156 SER cc_start: 0.4804 (OUTLIER) cc_final: 0.4480 (m) REVERT: J 93 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7167 (p0) REVERT: K 93 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7384 (p0) REVERT: L 93 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7186 (p0) outliers start: 39 outliers final: 23 residues processed: 260 average time/residue: 1.2332 time to fit residues: 350.0358 Evaluate side-chains 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119576 restraints weight = 10801.733| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.92 r_work: 0.3208 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12972 Z= 0.185 Angle : 0.652 8.711 17670 Z= 0.330 Chirality : 0.043 0.134 1824 Planarity : 0.004 0.033 2244 Dihedral : 8.529 80.893 1802 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.51 % Allowed : 15.23 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1602 helix: 3.20 (0.19), residues: 678 sheet: 0.43 (0.29), residues: 234 loop : -0.12 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.002 0.001 HIS B 58 PHE 0.017 0.002 PHE D 48 TYR 0.011 0.002 TYR J 108 ARG 0.003 0.000 ARG H 112 Details of bonding type rmsd hydrogen bonds : bond 0.07847 ( 774) hydrogen bonds : angle 4.85577 ( 2196) covalent geometry : bond 0.00395 (12966) covalent geometry : angle 0.65218 (17670) Misc. bond : bond 0.02611 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 156 SER cc_start: 0.4836 (OUTLIER) cc_final: 0.4517 (m) REVERT: C 156 SER cc_start: 0.4766 (OUTLIER) cc_final: 0.4498 (m) REVERT: D 93 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7412 (p0) REVERT: E 93 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7187 (p0) REVERT: F 20 ARG cc_start: 0.7964 (ttt-90) cc_final: 0.7300 (ttt180) REVERT: F 93 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7185 (p0) REVERT: G 156 SER cc_start: 0.4772 (OUTLIER) cc_final: 0.4499 (m) REVERT: H 156 SER cc_start: 0.4849 (OUTLIER) cc_final: 0.4527 (m) REVERT: J 20 ARG cc_start: 0.7965 (ttt-90) cc_final: 0.7304 (ttt180) REVERT: J 93 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7180 (p0) REVERT: K 93 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7421 (p0) REVERT: L 93 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7193 (p0) outliers start: 44 outliers final: 29 residues processed: 263 average time/residue: 1.2046 time to fit residues: 345.7397 Evaluate side-chains 270 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121499 restraints weight = 10865.045| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.92 r_work: 0.3243 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12972 Z= 0.157 Angle : 0.598 6.464 17670 Z= 0.302 Chirality : 0.042 0.132 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.374 79.336 1802 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.87 % Allowed : 15.55 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1602 helix: 3.35 (0.18), residues: 678 sheet: 0.43 (0.28), residues: 234 loop : -0.08 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS C 46 PHE 0.017 0.002 PHE D 48 TYR 0.009 0.002 TYR K 108 ARG 0.002 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.06998 ( 774) hydrogen bonds : angle 4.68395 ( 2196) covalent geometry : bond 0.00338 (12966) covalent geometry : angle 0.59837 (17670) Misc. bond : bond 0.02090 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.333 Fit side-chains REVERT: A 156 SER cc_start: 0.4780 (OUTLIER) cc_final: 0.4444 (m) REVERT: C 156 SER cc_start: 0.4775 (OUTLIER) cc_final: 0.4469 (m) REVERT: D 93 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7390 (p0) REVERT: E 93 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7167 (p0) REVERT: F 20 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7314 (ttt180) REVERT: F 93 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7171 (p0) REVERT: G 86 ARG cc_start: 0.7210 (mtt-85) cc_final: 0.6816 (mtm110) REVERT: G 156 SER cc_start: 0.4755 (OUTLIER) cc_final: 0.4456 (m) REVERT: J 93 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7171 (p0) REVERT: K 93 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7359 (p0) REVERT: L 93 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7166 (p0) outliers start: 36 outliers final: 23 residues processed: 257 average time/residue: 1.2398 time to fit residues: 347.9111 Evaluate side-chains 259 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119616 restraints weight = 10852.411| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.93 r_work: 0.3215 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12972 Z= 0.186 Angle : 0.660 10.006 17670 Z= 0.334 Chirality : 0.043 0.133 1824 Planarity : 0.004 0.033 2244 Dihedral : 8.517 80.879 1802 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.95 % Allowed : 15.79 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1602 helix: 3.17 (0.19), residues: 678 sheet: 0.46 (0.29), residues: 234 loop : -0.15 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.002 0.001 HIS B 58 PHE 0.017 0.002 PHE D 48 TYR 0.012 0.002 TYR J 108 ARG 0.003 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.07832 ( 774) hydrogen bonds : angle 4.86600 ( 2196) covalent geometry : bond 0.00399 (12966) covalent geometry : angle 0.66039 (17670) Misc. bond : bond 0.02587 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 156 SER cc_start: 0.4801 (OUTLIER) cc_final: 0.4473 (m) REVERT: C 156 SER cc_start: 0.4727 (OUTLIER) cc_final: 0.4439 (m) REVERT: D 93 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7414 (p0) REVERT: E 93 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7183 (p0) REVERT: F 20 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7307 (ttt180) REVERT: F 93 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7199 (p0) REVERT: G 82 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5847 (t70) REVERT: G 156 SER cc_start: 0.4706 (OUTLIER) cc_final: 0.4419 (m) REVERT: J 20 ARG cc_start: 0.7969 (ttt-90) cc_final: 0.7307 (ttt180) REVERT: J 93 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (p0) REVERT: K 93 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7418 (p0) REVERT: L 93 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7185 (p0) outliers start: 37 outliers final: 25 residues processed: 263 average time/residue: 1.2253 time to fit residues: 352.0621 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 81 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120000 restraints weight = 10926.169| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.93 r_work: 0.3216 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12972 Z= 0.177 Angle : 0.638 9.662 17670 Z= 0.324 Chirality : 0.042 0.133 1824 Planarity : 0.004 0.033 2244 Dihedral : 8.497 80.482 1802 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 15.31 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1602 helix: 3.19 (0.18), residues: 678 sheet: 0.46 (0.29), residues: 234 loop : -0.15 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.002 0.001 HIS B 58 PHE 0.017 0.002 PHE D 48 TYR 0.011 0.002 TYR J 108 ARG 0.003 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.07629 ( 774) hydrogen bonds : angle 4.82601 ( 2196) covalent geometry : bond 0.00379 (12966) covalent geometry : angle 0.63845 (17670) Misc. bond : bond 0.02480 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13913.71 seconds wall clock time: 238 minutes 27.53 seconds (14307.53 seconds total)