Starting phenix.real_space_refine on Thu May 15 07:50:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnv_17786/05_2025/8pnv_17786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnv_17786/05_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_17786/05_2025/8pnv_17786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnv_17786/05_2025/8pnv_17786.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnv_17786/05_2025/8pnv_17786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnv_17786/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.20, per 1000 atoms: 0.40 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: 2.92 Conformation dependent library (CDL) restraints added in 1.5 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: 1.44 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: 3.81 Time building geometry restraints manager: 3.44 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: 0.11 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: 7.610 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 26.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- 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 : 1.318 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: 1.3115 time to fit residues: 421.2618 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 : 1.276 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116430 restraints weight = 10554.488| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.92 r_work: 0.3172 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.20 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 : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7375 (mtt-85) REVERT: B 86 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7424 (mtt-85) REVERT: E 93 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7274 (p0) REVERT: F 93 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7268 (p0) REVERT: H 86 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7355 (mtt-85) REVERT: I 86 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7381 (mtt-85) REVERT: J 93 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7292 (p0) REVERT: L 93 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7290 (p0) outliers start: 70 outliers final: 44 residues processed: 300 average time/residue: 1.2783 time to fit residues: 416.1782 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 : 1.312 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.146449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119645 restraints weight = 10757.176| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.94 r_work: 0.3212 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1111 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= 0.167 Angle : 0.612 5.955 17670 Z= 0.313 Chirality : 0.042 0.131 1824 Planarity : 0.004 0.033 2244 Dihedral : 9.420 79.923 1848 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 : 2.95 % Allowed : 16.19 % 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: 2.22 (0.20), residues: 1602 helix: 3.27 (0.19), residues: 678 sheet: 0.50 (0.29), residues: 228 loop : 0.01 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 54 HIS 0.002 0.001 HIS F 58 PHE 0.017 0.002 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 0.07406 ( 774) hydrogen bonds : angle 4.78168 ( 2196) covalent geometry : bond 0.00353 (12966) covalent geometry : angle 0.61231 (17670) Misc. bond : bond 0.02374 ( 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 284 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7262 (mtt-85) REVERT: D 93 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7390 (p0) REVERT: F 107 GLU cc_start: 0.7173 (tt0) cc_final: 0.6971 (tt0) REVERT: K 93 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7371 (p0) outliers start: 37 outliers final: 17 residues processed: 269 average time/residue: 1.3103 time to fit residues: 381.7568 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118179 restraints weight = 10600.071| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.93 r_work: 0.3190 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12972 Z= 0.190 Angle : 0.651 6.750 17670 Z= 0.333 Chirality : 0.043 0.131 1824 Planarity : 0.005 0.035 2244 Dihedral : 8.824 81.135 1806 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.39 % Allowed : 14.75 % 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: 2.07 (0.20), residues: 1602 helix: 3.13 (0.19), residues: 678 sheet: 0.49 (0.29), residues: 228 loop : -0.11 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 54 HIS 0.002 0.001 HIS B 58 PHE 0.018 0.002 PHE D 48 TYR 0.010 0.002 TYR K 96 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.08065 ( 774) hydrogen bonds : angle 4.90154 ( 2196) covalent geometry : bond 0.00400 (12966) covalent geometry : angle 0.65067 (17670) Misc. bond : bond 0.02610 ( 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 293 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7303 (mtt-85) REVERT: D 93 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7396 (p0) REVERT: E 93 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7162 (p0) REVERT: F 93 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7158 (p0) REVERT: J 93 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7173 (p0) REVERT: K 93 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7394 (p0) REVERT: L 93 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7163 (p0) outliers start: 55 outliers final: 32 residues processed: 275 average time/residue: 1.2321 time to fit residues: 368.9624 Evaluate side-chains 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain B residue 82 ASP 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 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 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 13 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 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 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 = 0.3658 r_free = 0.3658 target = 0.146812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120193 restraints weight = 10769.516| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.95 r_work: 0.3218 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12972 Z= 0.161 Angle : 0.603 6.002 17670 Z= 0.305 Chirality : 0.042 0.131 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.627 79.670 1806 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 15.95 % Favored : 81.02 % 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: 2.18 (0.20), residues: 1602 helix: 3.30 (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 F 54 HIS 0.001 0.000 HIS J 58 PHE 0.017 0.002 PHE D 48 TYR 0.008 0.001 TYR K 96 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.07155 ( 774) hydrogen bonds : angle 4.71129 ( 2196) covalent geometry : bond 0.00343 (12966) covalent geometry : angle 0.60317 (17670) Misc. bond : bond 0.02072 ( 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 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7249 (mtt-85) REVERT: D 93 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7365 (p0) REVERT: E 93 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7152 (p0) REVERT: F 93 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7150 (p0) REVERT: J 93 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7164 (p0) REVERT: K 93 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7347 (p0) REVERT: L 93 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7150 (p0) outliers start: 38 outliers final: 19 residues processed: 255 average time/residue: 1.3322 time to fit residues: 367.9115 Evaluate side-chains 255 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 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: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.143145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116857 restraints weight = 10653.896| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 0.92 r_work: 0.3185 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12972 Z= 0.241 Angle : 0.724 7.282 17670 Z= 0.377 Chirality : 0.045 0.136 1824 Planarity : 0.005 0.043 2244 Dihedral : 9.058 82.792 1806 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.31 % Allowed : 15.07 % Favored : 80.62 % 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: 1.79 (0.20), residues: 1602 helix: 2.90 (0.19), residues: 678 sheet: 0.38 (0.29), residues: 234 loop : -0.27 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 54 HIS 0.003 0.001 HIS H 12 PHE 0.019 0.003 PHE D 48 TYR 0.015 0.003 TYR B 103 ARG 0.004 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.09015 ( 774) hydrogen bonds : angle 5.09348 ( 2196) covalent geometry : bond 0.00517 (12966) covalent geometry : angle 0.72426 (17670) Misc. bond : bond 0.02515 ( 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 285 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 1.306 Fit side-chains REVERT: A 86 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7381 (mtt-85) REVERT: A 156 SER cc_start: 0.4814 (OUTLIER) cc_final: 0.4541 (m) REVERT: C 156 SER cc_start: 0.4763 (OUTLIER) cc_final: 0.4556 (m) REVERT: D 93 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (p0) REVERT: E 93 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7193 (p0) REVERT: F 93 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7174 (p0) REVERT: G 156 SER cc_start: 0.4742 (OUTLIER) cc_final: 0.4520 (m) REVERT: H 156 SER cc_start: 0.4789 (OUTLIER) cc_final: 0.4514 (m) REVERT: J 93 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7176 (p0) REVERT: K 93 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7391 (p0) REVERT: L 93 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7191 (p0) outliers start: 54 outliers final: 28 residues processed: 268 average time/residue: 1.3408 time to fit residues: 389.6014 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 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 82 ASP Chi-restraints excluded: chain J residue 13 VAL 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: 0.8980 chunk 126 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118374 restraints weight = 10612.483| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.91 r_work: 0.3206 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1228 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= 0.195 Angle : 0.661 6.234 17670 Z= 0.339 Chirality : 0.043 0.132 1824 Planarity : 0.005 0.037 2244 Dihedral : 8.911 81.392 1806 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.51 % Allowed : 15.39 % Favored : 81.10 % 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: 1.89 (0.20), residues: 1602 helix: 3.05 (0.19), residues: 678 sheet: 0.38 (0.29), residues: 234 loop : -0.28 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 54 HIS 0.002 0.001 HIS I 58 PHE 0.018 0.002 PHE D 48 TYR 0.010 0.002 TYR D 96 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.08125 ( 774) hydrogen bonds : angle 4.93551 ( 2196) covalent geometry : bond 0.00415 (12966) covalent geometry : angle 0.66079 (17670) Misc. bond : bond 0.02687 ( 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 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7352 (mtt-85) REVERT: A 156 SER cc_start: 0.4828 (OUTLIER) cc_final: 0.4517 (m) REVERT: C 156 SER cc_start: 0.4759 (OUTLIER) cc_final: 0.4509 (m) REVERT: D 93 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7403 (p0) REVERT: E 93 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7174 (p0) REVERT: F 93 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7160 (p0) REVERT: G 156 SER cc_start: 0.4773 (OUTLIER) cc_final: 0.4517 (m) REVERT: H 156 SER cc_start: 0.4845 (OUTLIER) cc_final: 0.4531 (m) REVERT: J 93 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7168 (p0) REVERT: K 93 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7396 (p0) REVERT: L 93 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7170 (p0) outliers start: 44 outliers final: 28 residues processed: 261 average time/residue: 1.2998 time to fit residues: 367.9512 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 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 82 ASP Chi-restraints excluded: chain J residue 13 VAL 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: 2.9990 chunk 115 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.145009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118916 restraints weight = 10588.559| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.91 r_work: 0.3205 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12972 Z= 0.185 Angle : 0.649 5.945 17670 Z= 0.331 Chirality : 0.043 0.131 1824 Planarity : 0.005 0.032 2244 Dihedral : 8.840 80.867 1806 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.67 % Allowed : 15.39 % Favored : 80.94 % 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: 1.92 (0.20), residues: 1602 helix: 3.11 (0.19), residues: 678 sheet: 0.36 (0.29), residues: 234 loop : -0.29 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 54 HIS 0.002 0.001 HIS I 58 PHE 0.018 0.002 PHE D 48 TYR 0.010 0.002 TYR K 96 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.07887 ( 774) hydrogen bonds : angle 4.88908 ( 2196) covalent geometry : bond 0.00395 (12966) covalent geometry : angle 0.64887 (17670) Misc. bond : bond 0.02544 ( 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 277 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7323 (mtt-85) REVERT: A 156 SER cc_start: 0.4766 (OUTLIER) cc_final: 0.4447 (m) REVERT: C 156 SER cc_start: 0.4742 (OUTLIER) cc_final: 0.4466 (m) REVERT: D 93 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7420 (p0) REVERT: E 93 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7155 (p0) REVERT: F 20 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7370 (ttt180) REVERT: F 93 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7173 (p0) REVERT: G 156 SER cc_start: 0.4737 (OUTLIER) cc_final: 0.4462 (m) REVERT: H 156 SER cc_start: 0.4758 (OUTLIER) cc_final: 0.4433 (m) REVERT: J 20 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7383 (ttt180) REVERT: J 93 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7177 (p0) REVERT: K 93 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7412 (p0) REVERT: L 93 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7160 (p0) outliers start: 46 outliers final: 30 residues processed: 265 average time/residue: 1.2768 time to fit residues: 367.2187 Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 86 ARG 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 13 VAL 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: 1.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121113 restraints weight = 10660.239| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.92 r_work: 0.3243 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1301 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= 0.159 Angle : 0.612 9.332 17670 Z= 0.308 Chirality : 0.042 0.129 1824 Planarity : 0.004 0.031 2244 Dihedral : 8.624 79.342 1806 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.19 % Allowed : 15.71 % Favored : 81.10 % 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: 3.27 (0.19), residues: 678 sheet: 0.41 (0.29), residues: 234 loop : -0.20 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 54 HIS 0.001 0.000 HIS G 3 PHE 0.017 0.002 PHE D 48 TYR 0.008 0.002 TYR L 96 ARG 0.002 0.000 ARG H 112 Details of bonding type rmsd hydrogen bonds : bond 0.07000 ( 774) hydrogen bonds : angle 4.71260 ( 2196) covalent geometry : bond 0.00346 (12966) covalent geometry : angle 0.61218 (17670) Misc. bond : bond 0.02068 ( 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 274 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.409 Fit side-chains REVERT: A 82 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5645 (t0) REVERT: C 156 SER cc_start: 0.4733 (OUTLIER) cc_final: 0.4433 (m) REVERT: D 93 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 93 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7145 (p0) REVERT: F 20 ARG cc_start: 0.7986 (ttt-90) cc_final: 0.7403 (ttt180) REVERT: F 93 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7150 (p0) REVERT: G 86 ARG cc_start: 0.7310 (mtt-85) cc_final: 0.6879 (mtm110) REVERT: G 156 SER cc_start: 0.4710 (OUTLIER) cc_final: 0.4408 (m) REVERT: H 82 ASP cc_start: 0.5969 (OUTLIER) cc_final: 0.5644 (t0) REVERT: H 156 SER cc_start: 0.4731 (OUTLIER) cc_final: 0.4403 (m) REVERT: J 20 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7408 (ttt180) REVERT: J 93 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7165 (p0) REVERT: K 93 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7369 (p0) REVERT: L 93 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7154 (p0) outliers start: 40 outliers final: 20 residues processed: 263 average time/residue: 1.2310 time to fit residues: 352.0916 Evaluate side-chains 255 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 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 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 H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 13 VAL 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: 6.9990 chunk 119 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119398 restraints weight = 10763.987| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.91 r_work: 0.3208 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1274 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= 0.200 Angle : 0.674 9.340 17670 Z= 0.345 Chirality : 0.043 0.132 1824 Planarity : 0.005 0.036 2244 Dihedral : 8.841 81.435 1806 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.63 % Allowed : 16.43 % Favored : 80.94 % 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: 1.92 (0.20), residues: 1602 helix: 3.07 (0.19), residues: 678 sheet: 0.42 (0.29), residues: 234 loop : -0.27 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 54 HIS 0.002 0.001 HIS I 58 PHE 0.017 0.002 PHE D 48 TYR 0.010 0.002 TYR K 96 ARG 0.003 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.08179 ( 774) hydrogen bonds : angle 4.94985 ( 2196) covalent geometry : bond 0.00427 (12966) covalent geometry : angle 0.67423 (17670) Misc. bond : bond 0.02622 ( 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 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: C 156 SER cc_start: 0.4712 (OUTLIER) cc_final: 0.4430 (m) REVERT: D 93 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7428 (p0) REVERT: E 93 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7195 (p0) REVERT: F 20 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7355 (ttt180) REVERT: F 93 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7214 (p0) REVERT: G 156 SER cc_start: 0.4721 (OUTLIER) cc_final: 0.4441 (m) REVERT: H 156 SER cc_start: 0.4734 (OUTLIER) cc_final: 0.4431 (m) REVERT: J 20 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7356 (ttt180) REVERT: J 93 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7226 (p0) REVERT: K 93 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7428 (p0) REVERT: L 93 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7189 (p0) outliers start: 33 outliers final: 24 residues processed: 258 average time/residue: 1.2942 time to fit residues: 362.0661 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 : 1.280 ------------------------------------------------------------------------------- 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 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 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 82 ASP Chi-restraints excluded: chain J residue 13 VAL 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: 0.5980 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120324 restraints weight = 10719.377| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.92 r_work: 0.3232 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12972 Z= 0.167 Angle : 0.625 9.967 17670 Z= 0.316 Chirality : 0.042 0.128 1824 Planarity : 0.004 0.032 2244 Dihedral : 8.672 79.824 1806 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.63 % Allowed : 16.35 % Favored : 81.02 % 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: 2.02 (0.20), residues: 1602 helix: 3.19 (0.19), residues: 678 sheet: 0.42 (0.29), residues: 234 loop : -0.24 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 54 HIS 0.001 0.000 HIS B 58 PHE 0.017 0.002 PHE D 48 TYR 0.008 0.002 TYR D 96 ARG 0.002 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.07312 ( 774) hydrogen bonds : angle 4.78391 ( 2196) covalent geometry : bond 0.00360 (12966) covalent geometry : angle 0.62492 (17670) Misc. bond : bond 0.02175 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12900.89 seconds wall clock time: 222 minutes 11.94 seconds (13331.94 seconds total)