Starting phenix.real_space_refine on Mon Dec 30 10:26:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnv_17786/12_2024/8pnv_17786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnv_17786/12_2024/8pnv_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_17786/12_2024/8pnv_17786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnv_17786/12_2024/8pnv_17786.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnv_17786/12_2024/8pnv_17786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnv_17786/12_2024/8pnv_17786.cif" } resolution = 2.048 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 60 5.16 5 C 8202 2.51 5 N 2106 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13098 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: D, F, K, J, L, C, B, G, I, H Time building chain proxies: 6.40, per 1000 atoms: 0.49 Number of scatterers: 13098 At special positions: 0 Unit cell: (79.2, 81.18, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 60 16.00 O 2724 8.00 N 2106 7.00 C 8202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.8 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: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 155 Proline residue: A 134 - end of helix removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Proline residue: B 61 - end of helix Processing helix chain 'B' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 155 Proline residue: B 134 - end of helix removed outlier: 3.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 Proline residue: C 61 - end of helix Processing helix chain 'C' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 155 Proline residue: C 134 - end of helix removed outlier: 3.654A pdb=" N LEU C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 75 Proline residue: G 61 - end of helix Processing helix chain 'G' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY G 79 " --> pdb=" O PRO G 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 79' Processing helix chain 'G' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN G 107 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 155 Proline residue: G 134 - end of helix removed outlier: 3.654A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 75 Proline residue: H 61 - end of helix Processing helix chain 'H' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 79' Processing helix chain 'H' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN H 107 " --> pdb=" O TYR H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 155 Proline residue: H 134 - end of helix removed outlier: 3.654A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 75 Proline residue: I 61 - end of helix Processing helix chain 'I' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY I 79 " --> pdb=" O PRO I 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN I 107 " --> pdb=" O TYR I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 155 Proline residue: I 134 - end of helix removed outlier: 3.655A pdb=" N LEU I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'K' and resid 63 through 66 Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'L' and resid 63 through 66 Processing helix chain 'L' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU A 36 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 43 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 38 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU B 36 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 43 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 38 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU C 36 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 43 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 38 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL D 35 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL E 35 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR E 51 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL F 35 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR F 51 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'G' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU G 36 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE G 43 " --> pdb=" O GLU G 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 38 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU H 36 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE H 43 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE H 38 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU I 36 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE I 43 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE I 38 " --> pdb=" O TYR I 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL J 35 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR J 51 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AC1, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL K 35 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP K 37 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 12 through 14 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL L 35 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR L 51 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 14 810 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 3.73 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 7.320 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 28.850 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- 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 12966 Z= 0.264 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 *********************** 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 : 1.361 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: 1.2951 time to fit residues: 417.8848 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 : 1.511 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 12966 Z= 0.417 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 *********************** 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 : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7290 (mtt-85) REVERT: B 86 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7277 (mtt-85) REVERT: E 93 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7253 (p0) REVERT: F 93 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7246 (p0) REVERT: H 86 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7291 (mtt-85) REVERT: I 86 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7246 (mtt-85) REVERT: J 93 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7260 (p0) REVERT: L 93 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7261 (p0) outliers start: 70 outliers final: 44 residues processed: 300 average time/residue: 1.2752 time to fit residues: 416.1129 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 : 1.374 ------------------------------------------------------------------------------- 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 78 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12966 Z= 0.217 Angle : 0.588 5.936 17670 Z= 0.299 Chirality : 0.041 0.133 1824 Planarity : 0.004 0.032 2244 Dihedral : 9.293 78.985 1848 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.87 % Allowed : 16.11 % 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: 2.34 (0.20), residues: 1602 helix: 3.38 (0.19), residues: 678 sheet: 0.51 (0.29), residues: 228 loop : 0.06 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 54 HIS 0.001 0.000 HIS F 58 PHE 0.017 0.001 PHE D 48 TYR 0.007 0.001 TYR E 96 ARG 0.002 0.000 ARG A 112 *********************** 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 279 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: C 7 ARG cc_start: 0.8013 (ttp-110) cc_final: 0.7798 (ttp80) REVERT: D 93 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7262 (p0) REVERT: J 53 ASN cc_start: 0.6922 (t0) cc_final: 0.6719 (t0) REVERT: K 93 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7278 (p0) outliers start: 36 outliers final: 17 residues processed: 264 average time/residue: 1.3320 time to fit residues: 382.5934 Evaluate side-chains 255 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 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 140 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12966 Z= 0.219 Angle : 0.593 5.971 17670 Z= 0.298 Chirality : 0.041 0.133 1824 Planarity : 0.004 0.029 2244 Dihedral : 8.539 79.422 1806 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 16.19 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1602 helix: 3.38 (0.18), residues: 678 sheet: 0.48 (0.28), residues: 228 loop : 0.06 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 54 HIS 0.001 0.000 HIS I 58 PHE 0.017 0.001 PHE K 48 TYR 0.007 0.001 TYR D 96 ARG 0.002 0.000 ARG H 112 *********************** 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 275 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.337 Fit side-chains REVERT: E 93 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7098 (p0) REVERT: F 53 ASN cc_start: 0.7000 (t0) cc_final: 0.6792 (t0) REVERT: F 93 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7101 (p0) REVERT: J 53 ASN cc_start: 0.6952 (t0) cc_final: 0.6716 (t0) REVERT: J 93 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7104 (p0) REVERT: K 93 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7268 (p0) REVERT: L 93 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7096 (p0) outliers start: 38 outliers final: 16 residues processed: 260 average time/residue: 1.2720 time to fit residues: 360.4918 Evaluate side-chains 252 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.003 0.048 12966 Z= 0.209 Angle : 0.577 6.044 17670 Z= 0.289 Chirality : 0.041 0.132 1824 Planarity : 0.004 0.029 2244 Dihedral : 8.260 78.949 1802 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.79 % Allowed : 16.11 % 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: 2.37 (0.20), residues: 1602 helix: 3.45 (0.18), residues: 678 sheet: 0.39 (0.28), residues: 234 loop : 0.09 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 54 HIS 0.001 0.000 HIS I 58 PHE 0.017 0.001 PHE K 48 TYR 0.008 0.001 TYR K 108 ARG 0.002 0.000 ARG H 112 *********************** 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 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: E 93 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7086 (p0) REVERT: J 53 ASN cc_start: 0.6933 (t0) cc_final: 0.6704 (t0) REVERT: K 93 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7241 (p0) REVERT: L 93 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7086 (p0) outliers start: 35 outliers final: 23 residues processed: 262 average time/residue: 1.2544 time to fit residues: 359.0454 Evaluate side-chains 253 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 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 B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain 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 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 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 87 LEU 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 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 K 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.216 Angle : 0.588 6.298 17670 Z= 0.294 Chirality : 0.041 0.131 1824 Planarity : 0.004 0.029 2244 Dihedral : 8.269 79.256 1802 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.19 % Allowed : 15.47 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1602 helix: 3.42 (0.18), residues: 678 sheet: 0.40 (0.28), residues: 234 loop : 0.06 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS I 58 PHE 0.017 0.001 PHE K 48 TYR 0.008 0.001 TYR K 108 ARG 0.002 0.000 ARG H 112 *********************** 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 274 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: E 93 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7093 (p0) REVERT: F 20 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7481 (ttt180) REVERT: F 93 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7093 (p0) REVERT: J 53 ASN cc_start: 0.6964 (t0) cc_final: 0.6738 (t0) REVERT: J 93 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7099 (p0) REVERT: L 93 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7094 (p0) outliers start: 40 outliers final: 25 residues processed: 263 average time/residue: 1.2476 time to fit residues: 358.4354 Evaluate side-chains 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain 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 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 38 ILE 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 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 145 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.0000 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- 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 K 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12966 Z= 0.201 Angle : 0.565 8.387 17670 Z= 0.280 Chirality : 0.041 0.130 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.164 78.232 1802 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.47 % Allowed : 15.95 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.20), residues: 1602 helix: 3.55 (0.18), residues: 678 sheet: 0.42 (0.28), residues: 234 loop : 0.12 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 54 HIS 0.001 0.000 HIS F 58 PHE 0.016 0.001 PHE K 48 TYR 0.006 0.001 TYR K 108 ARG 0.001 0.000 ARG C 86 *********************** 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 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: F 20 ARG cc_start: 0.7809 (ttt-90) cc_final: 0.7473 (ttt180) REVERT: F 93 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7060 (p0) REVERT: J 20 ARG cc_start: 0.7803 (ttt-90) cc_final: 0.7474 (ttt180) REVERT: J 93 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7076 (p0) outliers start: 31 outliers final: 24 residues processed: 256 average time/residue: 1.2767 time to fit residues: 356.3824 Evaluate side-chains 253 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER 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 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 L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER 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 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.0670 chunk 144 optimal weight: 0.8980 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 53 ASN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.213 Angle : 0.588 8.998 17670 Z= 0.292 Chirality : 0.041 0.130 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.195 78.933 1802 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.47 % Allowed : 15.63 % Favored : 81.90 % 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: 2.40 (0.20), residues: 1602 helix: 3.48 (0.18), residues: 678 sheet: 0.41 (0.28), residues: 234 loop : 0.10 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 54 HIS 0.001 0.000 HIS B 58 PHE 0.016 0.001 PHE K 48 TYR 0.008 0.001 TYR K 108 ARG 0.002 0.000 ARG C 86 *********************** 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 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 156 SER cc_start: 0.4603 (OUTLIER) cc_final: 0.4359 (m) REVERT: E 93 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7088 (p0) REVERT: F 20 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7474 (ttt180) REVERT: F 93 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7076 (p0) REVERT: H 156 SER cc_start: 0.4602 (OUTLIER) cc_final: 0.4356 (m) REVERT: J 20 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7457 (ttt180) REVERT: J 93 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7105 (p0) REVERT: L 93 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7090 (p0) outliers start: 31 outliers final: 24 residues processed: 257 average time/residue: 1.1886 time to fit residues: 334.0626 Evaluate side-chains 259 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain 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 38 ILE 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 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 131 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 144 optimal weight: 0.0020 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 53 ASN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.206 Angle : 0.568 6.788 17670 Z= 0.283 Chirality : 0.041 0.130 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.178 78.646 1802 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.87 % Allowed : 15.31 % Favored : 81.82 % 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: 2.44 (0.20), residues: 1602 helix: 3.51 (0.18), residues: 678 sheet: 0.45 (0.28), residues: 234 loop : 0.12 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 54 HIS 0.001 0.000 HIS I 58 PHE 0.016 0.001 PHE K 48 TYR 0.007 0.001 TYR F 108 ARG 0.002 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.500 Fit side-chains REVERT: A 82 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5606 (t0) REVERT: A 156 SER cc_start: 0.4737 (OUTLIER) cc_final: 0.4454 (m) REVERT: C 156 SER cc_start: 0.4633 (OUTLIER) cc_final: 0.4393 (m) REVERT: E 93 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7082 (p0) REVERT: F 20 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7466 (ttt180) REVERT: F 93 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7072 (p0) REVERT: G 86 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6983 (mtm110) REVERT: G 156 SER cc_start: 0.4501 (OUTLIER) cc_final: 0.4265 (m) REVERT: H 156 SER cc_start: 0.4747 (OUTLIER) cc_final: 0.4464 (m) REVERT: J 20 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7449 (ttt180) REVERT: J 93 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7111 (p0) REVERT: L 93 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7084 (p0) outliers start: 36 outliers final: 23 residues processed: 260 average time/residue: 1.2209 time to fit residues: 346.9366 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 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 38 ILE 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 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 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 53 ASN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12966 Z= 0.248 Angle : 0.644 10.347 17670 Z= 0.323 Chirality : 0.042 0.132 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.367 80.160 1802 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.63 % Allowed : 15.71 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1602 helix: 3.31 (0.18), residues: 678 sheet: 0.41 (0.29), residues: 234 loop : 0.02 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.002 0.001 HIS I 58 PHE 0.017 0.002 PHE K 48 TYR 0.010 0.002 TYR J 108 ARG 0.003 0.000 ARG H 112 ********************** 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 265 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 156 SER cc_start: 0.4749 (OUTLIER) cc_final: 0.4471 (m) REVERT: C 156 SER cc_start: 0.4642 (OUTLIER) cc_final: 0.4413 (m) REVERT: E 93 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7117 (p0) REVERT: F 20 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7456 (ttt180) REVERT: F 93 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7120 (p0) REVERT: G 156 SER cc_start: 0.4651 (OUTLIER) cc_final: 0.4419 (m) REVERT: H 156 SER cc_start: 0.4768 (OUTLIER) cc_final: 0.4489 (m) REVERT: J 93 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7141 (p0) REVERT: L 93 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7113 (p0) outliers start: 33 outliers final: 24 residues processed: 259 average time/residue: 1.2735 time to fit residues: 359.2118 Evaluate side-chains 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 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 38 ILE 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 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 131 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 53 ASN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120189 restraints weight = 10772.998| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.93 r_work: 0.3222 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12966 Z= 0.251 Angle : 0.628 9.540 17670 Z= 0.320 Chirality : 0.042 0.133 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.464 80.634 1802 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.63 % Allowed : 15.39 % Favored : 81.98 % 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: 2.15 (0.20), residues: 1602 helix: 3.22 (0.18), residues: 678 sheet: 0.43 (0.29), residues: 234 loop : -0.06 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.003 0.001 HIS I 58 PHE 0.017 0.002 PHE K 48 TYR 0.011 0.002 TYR J 108 ARG 0.002 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5873.06 seconds wall clock time: 105 minutes 40.77 seconds (6340.77 seconds total)