Starting phenix.real_space_refine on Mon Jul 28 16:37:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.map" model { file = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2025/7x5a_33013.cif" } resolution = 3.01 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 104 5.49 5 S 32 5.16 5 C 6510 2.51 5 N 1888 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 533 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1083 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A DT I 36 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT I 36 " occ=0.25 residue: pdb=" P A DA I 42 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA I 42 " occ=0.25 residue: pdb=" P A DA K 20 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA K 20 " occ=0.25 residue: pdb=" P A DT K 26 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT K 26 " occ=0.25 Time building chain proxies: 9.60, per 1000 atoms: 0.90 Number of scatterers: 10686 At special positions: 0 Unit cell: (98.77, 112.88, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 104 15.00 O 2152 8.00 N 1888 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 47.6% alpha, 11.8% beta 36 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.209A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'B' and resid 31 through 37 removed outlier: 3.570A pdb=" N ARG B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 113 removed outlier: 4.032A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.605A pdb=" N LEU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.607A pdb=" N LYS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 4.088A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 106 through 113 removed outlier: 3.868A pdb=" N LEU E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 132 removed outlier: 4.122A pdb=" N ASP E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.871A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.562A pdb=" N ALA F 121 " --> pdb=" O GLY F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 37 removed outlier: 3.701A pdb=" N ARG G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 106 through 113 removed outlier: 4.124A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.501A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 removed outlier: 3.871A pdb=" N ASP H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.766A pdb=" N ILE A 18 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS A 12 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 61 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 61 current: chain 'C' and resid 16 through 21 removed outlier: 3.507A pdb=" N VAL C 24 " --> pdb=" O VAL C 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 61 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 13 removed outlier: 3.628A pdb=" N THR E 8 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 18 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS E 12 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 29 current: chain 'E' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 61 current: chain 'F' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 61 current: chain 'G' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 29 current: chain 'G' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 61 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 57 through 61 356 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.45: 2025 1.45 - 1.57: 5887 1.57 - 1.69: 204 1.69 - 1.81: 56 Bond restraints: 11086 Sorted by residual: bond pdb=" N9 DA K 11 " pdb=" C1'A DA K 11 " ideal model delta sigma weight residual 1.460 1.502 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N9 DA K 13 " pdb=" C1'A DA K 13 " ideal model delta sigma weight residual 1.460 1.502 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" N9 DA K 27 " pdb=" C1'A DA K 27 " ideal model delta sigma weight residual 1.460 1.501 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 11081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 14129 0.84 - 1.68: 970 1.68 - 2.52: 256 2.52 - 3.35: 58 3.35 - 4.19: 26 Bond angle restraints: 15439 Sorted by residual: angle pdb=" C3'A DA K 13 " pdb=" C2'A DA K 13 " pdb=" C1'A DA K 13 " ideal model delta sigma weight residual 101.60 105.61 -4.01 1.50e+00 4.44e-01 7.15e+00 angle pdb=" C3'A DA J 25 " pdb=" C2'A DA J 25 " pdb=" C1'A DA J 25 " ideal model delta sigma weight residual 101.60 105.55 -3.95 1.50e+00 4.44e-01 6.93e+00 angle pdb=" C4'A DA K 13 " pdb=" C3'A DA K 13 " pdb=" O3'A DA K 13 " ideal model delta sigma weight residual 110.00 113.65 -3.65 1.50e+00 4.44e-01 5.91e+00 angle pdb=" C3'A DA J 32 " pdb=" C2'A DA J 32 " pdb=" C1'A DA J 32 " ideal model delta sigma weight residual 101.60 105.13 -3.53 1.50e+00 4.44e-01 5.54e+00 angle pdb=" C4 A DT K 26 " pdb=" C5 A DT K 26 " pdb=" C7 A DT K 26 " ideal model delta sigma weight residual 122.40 118.94 3.46 1.50e+00 4.44e-01 5.31e+00 ... (remaining 15434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 5939 31.37 - 62.74: 613 62.74 - 94.10: 18 94.10 - 125.47: 1 125.47 - 156.84: 2 Dihedral angle restraints: 6573 sinusoidal: 3484 harmonic: 3089 Sorted by residual: dihedral pdb=" C4'A DA I 20 " pdb=" C3'A DA I 20 " pdb=" O3'A DA I 20 " pdb=" P A DA I 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.16 156.84 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4'A DT L 44 " pdb=" C3'A DT L 44 " pdb=" O3'A DT L 44 " pdb=" P A DT L 45 " ideal model delta sinusoidal sigma weight residual 220.00 65.27 154.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA LYS F 129 " pdb=" C LYS F 129 " pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1156 0.028 - 0.056: 404 0.056 - 0.083: 116 0.083 - 0.111: 84 0.111 - 0.139: 43 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA ILE B 113 " pdb=" N ILE B 113 " pdb=" C ILE B 113 " pdb=" CB ILE B 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE D 113 " pdb=" N ILE D 113 " pdb=" C ILE D 113 " pdb=" CB ILE D 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE E 113 " pdb=" N ILE E 113 " pdb=" C ILE E 113 " pdb=" CB ILE E 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1800 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 38 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 39 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 113 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO F 114 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C LYS C 118 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 547 2.73 - 3.27: 9924 3.27 - 3.81: 18441 3.81 - 4.36: 22135 4.36 - 4.90: 36510 Nonbonded interactions: 87557 Sorted by model distance: nonbonded pdb=" O LYS H 118 " pdb=" OE1 GLU H 122 " model vdw 2.182 3.040 nonbonded pdb=" O VAL C 126 " pdb=" NZ LYS G 119 " model vdw 2.183 3.120 nonbonded pdb=" OP1A DA K 30 " pdb=" OG1 THR A 120 " model vdw 2.206 3.040 nonbonded pdb=" O ARG E 123 " pdb=" OE1 GLU E 127 " model vdw 2.241 3.040 nonbonded pdb=" O LYS H 118 " pdb=" N ALA H 121 " model vdw 2.248 3.120 ... (remaining 87552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 135) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 135) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 12 through 22 or resid 24 through 30 or resid 32 through 3 \ 6)) selection = (chain 'L' and (resid 21 through 24 or resid 26 through 32 or resid 34 through 4 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.92 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: 6.560 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.940 Find NCS groups from input model: 0.450 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.003 0.042 11086 Z= 0.133 Angle : 0.534 4.193 15439 Z= 0.310 Chirality : 0.040 0.139 1803 Planarity : 0.003 0.052 1598 Dihedral : 20.334 156.839 4583 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.22 (0.28), residues: 1067 helix: 1.12 (0.25), residues: 507 sheet: -1.52 (0.30), residues: 268 loop : 0.45 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 135 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE E 132 TYR 0.007 0.001 TYR C 36 ARG 0.003 0.000 ARG F 100 Details of bonding type rmsd hydrogen bonds : bond 0.13290 ( 428) hydrogen bonds : angle 5.89058 ( 1191) covalent geometry : bond 0.00280 (11086) covalent geometry : angle 0.53399 (15439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: B 70 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8079 (mm-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3266 time to fit residues: 93.6019 Evaluate side-chains 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN C 103 GLN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.181101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123050 restraints weight = 11168.256| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.14 r_work: 0.3298 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11086 Z= 0.163 Angle : 0.565 7.398 15439 Z= 0.307 Chirality : 0.039 0.150 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.719 151.636 2423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.18 % Allowed : 6.98 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.19 (0.28), residues: 1067 helix: 0.96 (0.24), residues: 510 sheet: -1.35 (0.29), residues: 278 loop : 0.62 (0.44), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.007 0.001 HIS B 58 PHE 0.010 0.002 PHE F 63 TYR 0.007 0.001 TYR F 36 ARG 0.006 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 428) hydrogen bonds : angle 4.61046 ( 1191) covalent geometry : bond 0.00378 (11086) covalent geometry : angle 0.56466 (15439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.152 Fit side-chains REVERT: B 68 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: C 112 LYS cc_start: 0.8097 (mptt) cc_final: 0.7818 (mptt) REVERT: C 122 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: D 106 ASP cc_start: 0.7876 (t0) cc_final: 0.7654 (t0) REVERT: E 109 THR cc_start: 0.7575 (m) cc_final: 0.7354 (p) REVERT: F 101 CYS cc_start: 0.6643 (m) cc_final: 0.6405 (m) REVERT: G 77 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7942 (ttp-170) outliers start: 11 outliers final: 4 residues processed: 186 average time/residue: 0.3582 time to fit residues: 84.5792 Evaluate side-chains 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain F residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123081 restraints weight = 11481.789| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.37 r_work: 0.3168 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.147 Angle : 0.536 6.354 15439 Z= 0.293 Chirality : 0.038 0.133 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.825 153.047 2423 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.83 % Allowed : 7.63 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.37 (0.27), residues: 1067 helix: 1.13 (0.24), residues: 496 sheet: -1.35 (0.28), residues: 280 loop : 0.77 (0.43), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.006 0.001 HIS H 58 PHE 0.008 0.002 PHE D 132 TYR 0.010 0.001 TYR F 36 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 428) hydrogen bonds : angle 4.28390 ( 1191) covalent geometry : bond 0.00341 (11086) covalent geometry : angle 0.53587 (15439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.072 Fit side-chains REVERT: B 68 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: C 32 MET cc_start: 0.7977 (mmt) cc_final: 0.7670 (mmt) REVERT: C 112 LYS cc_start: 0.8085 (mptt) cc_final: 0.7755 (mmtm) REVERT: C 122 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 106 ASP cc_start: 0.7859 (t0) cc_final: 0.7574 (t0) REVERT: D 129 LYS cc_start: 0.7931 (tppt) cc_final: 0.7693 (tppt) REVERT: E 32 MET cc_start: 0.7796 (mmm) cc_final: 0.7399 (mmm) REVERT: E 65 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8050 (mm-30) REVERT: E 100 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6740 (ttp80) REVERT: F 97 GLU cc_start: 0.7616 (mp0) cc_final: 0.6843 (mp0) REVERT: F 101 CYS cc_start: 0.6734 (m) cc_final: 0.6490 (m) REVERT: G 93 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7587 (pp) outliers start: 17 outliers final: 8 residues processed: 184 average time/residue: 0.3491 time to fit residues: 81.7008 Evaluate side-chains 179 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120347 restraints weight = 11447.523| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.14 r_work: 0.3231 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.137 Angle : 0.524 6.179 15439 Z= 0.287 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.031 1598 Dihedral : 23.816 152.938 2423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.04 % Allowed : 8.49 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.37 (0.27), residues: 1067 helix: 1.14 (0.24), residues: 498 sheet: -1.37 (0.28), residues: 280 loop : 0.76 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE F 63 TYR 0.005 0.001 TYR F 36 ARG 0.003 0.000 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 428) hydrogen bonds : angle 4.16849 ( 1191) covalent geometry : bond 0.00316 (11086) covalent geometry : angle 0.52439 (15439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 2.015 Fit side-chains REVERT: B 68 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: C 17 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 32 MET cc_start: 0.8006 (mmt) cc_final: 0.7724 (mmt) REVERT: C 112 LYS cc_start: 0.8103 (mptt) cc_final: 0.7729 (mptt) REVERT: C 122 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: D 106 ASP cc_start: 0.7865 (t0) cc_final: 0.7507 (t0) REVERT: D 129 LYS cc_start: 0.7861 (tppt) cc_final: 0.7342 (tptt) REVERT: E 32 MET cc_start: 0.7930 (mmm) cc_final: 0.7510 (mmm) REVERT: E 65 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8152 (mm-30) REVERT: E 100 ARG cc_start: 0.7071 (ttp80) cc_final: 0.6792 (ttp80) REVERT: E 118 LYS cc_start: 0.8002 (mptt) cc_final: 0.7726 (mtpp) REVERT: E 123 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7424 (mtp85) REVERT: F 101 CYS cc_start: 0.6685 (m) cc_final: 0.6454 (m) REVERT: G 93 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7478 (pp) outliers start: 19 outliers final: 11 residues processed: 186 average time/residue: 0.4678 time to fit residues: 110.7890 Evaluate side-chains 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN C 79 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114478 restraints weight = 11467.976| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.16 r_work: 0.3159 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11086 Z= 0.201 Angle : 0.586 6.863 15439 Z= 0.309 Chirality : 0.040 0.132 1803 Planarity : 0.004 0.033 1598 Dihedral : 23.948 153.714 2423 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.47 % Allowed : 9.34 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.21 (0.27), residues: 1067 helix: 0.99 (0.24), residues: 495 sheet: -1.43 (0.28), residues: 278 loop : 0.68 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 135 HIS 0.008 0.002 HIS H 58 PHE 0.013 0.002 PHE D 132 TYR 0.007 0.001 TYR F 36 ARG 0.008 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 428) hydrogen bonds : angle 4.30187 ( 1191) covalent geometry : bond 0.00483 (11086) covalent geometry : angle 0.58611 (15439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.003 Fit side-chains REVERT: C 17 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8240 (mt) REVERT: C 112 LYS cc_start: 0.8081 (mptt) cc_final: 0.7658 (mmtm) REVERT: C 122 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 106 ASP cc_start: 0.7897 (t0) cc_final: 0.7520 (t0) REVERT: D 129 LYS cc_start: 0.7874 (tppt) cc_final: 0.7360 (tptt) REVERT: E 65 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8160 (mm-30) REVERT: E 100 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6755 (ttp80) REVERT: F 101 CYS cc_start: 0.6680 (m) cc_final: 0.6430 (m) REVERT: G 93 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7561 (pp) outliers start: 23 outliers final: 12 residues processed: 190 average time/residue: 0.3597 time to fit residues: 87.0813 Evaluate side-chains 193 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115088 restraints weight = 11547.309| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.13 r_work: 0.3171 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11086 Z= 0.152 Angle : 0.541 6.334 15439 Z= 0.292 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.033 1598 Dihedral : 23.875 153.656 2423 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.26 % Allowed : 10.31 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.22 (0.27), residues: 1067 helix: 1.02 (0.24), residues: 496 sheet: -1.41 (0.28), residues: 280 loop : 0.68 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE E 132 TYR 0.006 0.001 TYR F 36 ARG 0.006 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 428) hydrogen bonds : angle 4.21591 ( 1191) covalent geometry : bond 0.00358 (11086) covalent geometry : angle 0.54066 (15439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.096 Fit side-chains REVERT: B 68 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: C 17 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 101 CYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6748 (m) REVERT: C 112 LYS cc_start: 0.8089 (mptt) cc_final: 0.7780 (tptp) REVERT: C 122 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: D 106 ASP cc_start: 0.7885 (t0) cc_final: 0.7520 (t0) REVERT: E 65 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8128 (mm-30) REVERT: E 100 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6945 (ttp80) REVERT: E 118 LYS cc_start: 0.8035 (mptt) cc_final: 0.7733 (mtpp) REVERT: E 123 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7393 (mtp85) REVERT: E 127 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6900 (mt-10) REVERT: F 101 CYS cc_start: 0.6779 (m) cc_final: 0.6535 (m) REVERT: G 93 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7574 (pp) outliers start: 21 outliers final: 11 residues processed: 188 average time/residue: 0.4894 time to fit residues: 119.2609 Evaluate side-chains 188 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN G 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.181952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124738 restraints weight = 11669.051| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.33 r_work: 0.3149 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11086 Z= 0.152 Angle : 0.541 6.323 15439 Z= 0.292 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.033 1598 Dihedral : 23.845 153.745 2423 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.15 % Allowed : 10.85 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.25 (0.27), residues: 1067 helix: 1.04 (0.24), residues: 501 sheet: -1.42 (0.28), residues: 280 loop : 0.71 (0.42), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE D 132 TYR 0.006 0.001 TYR F 36 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 428) hydrogen bonds : angle 4.16884 ( 1191) covalent geometry : bond 0.00358 (11086) covalent geometry : angle 0.54122 (15439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.349 Fit side-chains REVERT: B 68 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: C 17 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8151 (mt) REVERT: C 101 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6836 (m) REVERT: C 112 LYS cc_start: 0.8065 (mptt) cc_final: 0.7835 (tptp) REVERT: C 122 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: D 106 ASP cc_start: 0.7936 (t0) cc_final: 0.7676 (t0) REVERT: D 129 LYS cc_start: 0.8028 (tppt) cc_final: 0.7348 (tptt) REVERT: E 100 ARG cc_start: 0.7275 (ttp80) cc_final: 0.7052 (ttp80) REVERT: E 123 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7422 (mtp85) REVERT: E 127 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6910 (mt-10) REVERT: F 70 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8159 (mm-30) REVERT: F 101 CYS cc_start: 0.6994 (m) cc_final: 0.6766 (m) REVERT: G 93 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7697 (pp) outliers start: 20 outliers final: 12 residues processed: 188 average time/residue: 0.3540 time to fit residues: 85.5449 Evaluate side-chains 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119587 restraints weight = 11336.574| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.13 r_work: 0.3156 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11086 Z= 0.150 Angle : 0.543 6.291 15439 Z= 0.293 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.033 1598 Dihedral : 23.826 153.784 2423 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.36 % Allowed : 10.63 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.27 (0.27), residues: 1067 helix: 1.05 (0.24), residues: 501 sheet: -1.41 (0.28), residues: 280 loop : 0.73 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE B 63 TYR 0.006 0.001 TYR F 36 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 428) hydrogen bonds : angle 4.15070 ( 1191) covalent geometry : bond 0.00352 (11086) covalent geometry : angle 0.54270 (15439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.203 Fit side-chains REVERT: B 68 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: C 17 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 101 CYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6765 (m) REVERT: C 112 LYS cc_start: 0.8083 (mptt) cc_final: 0.7830 (tptp) REVERT: C 122 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: D 106 ASP cc_start: 0.7909 (t0) cc_final: 0.7645 (t0) REVERT: E 32 MET cc_start: 0.7775 (mmm) cc_final: 0.7362 (mmm) REVERT: E 100 ARG cc_start: 0.7238 (ttp80) cc_final: 0.7016 (ttp80) REVERT: E 118 LYS cc_start: 0.8051 (mptt) cc_final: 0.7789 (mtpp) REVERT: E 123 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7422 (mtp85) REVERT: F 101 CYS cc_start: 0.6887 (m) cc_final: 0.6663 (m) REVERT: G 93 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7710 (pp) outliers start: 22 outliers final: 12 residues processed: 181 average time/residue: 0.4051 time to fit residues: 93.5626 Evaluate side-chains 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120144 restraints weight = 11510.149| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.16 r_work: 0.3157 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.144 Angle : 0.539 6.187 15439 Z= 0.291 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.037 1598 Dihedral : 23.810 153.766 2423 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.15 % Allowed : 10.63 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.28 (0.27), residues: 1067 helix: 1.06 (0.24), residues: 500 sheet: -1.41 (0.28), residues: 280 loop : 0.75 (0.43), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE B 63 TYR 0.006 0.001 TYR F 36 ARG 0.007 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 428) hydrogen bonds : angle 4.14531 ( 1191) covalent geometry : bond 0.00337 (11086) covalent geometry : angle 0.53924 (15439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.128 Fit side-chains REVERT: B 68 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 17 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8127 (mt) REVERT: C 101 CYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6766 (m) REVERT: C 112 LYS cc_start: 0.8132 (mptt) cc_final: 0.7878 (tptp) REVERT: C 122 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 106 ASP cc_start: 0.7914 (t0) cc_final: 0.7648 (t0) REVERT: D 129 LYS cc_start: 0.7978 (tppt) cc_final: 0.7250 (tptt) REVERT: E 32 MET cc_start: 0.7782 (mmm) cc_final: 0.7371 (mmm) REVERT: E 100 ARG cc_start: 0.7274 (ttp80) cc_final: 0.7043 (ttp80) REVERT: E 118 LYS cc_start: 0.8071 (mptt) cc_final: 0.7809 (mtpp) REVERT: E 123 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7407 (mtp85) REVERT: F 101 CYS cc_start: 0.6866 (m) cc_final: 0.6640 (m) REVERT: G 93 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7700 (pp) outliers start: 20 outliers final: 13 residues processed: 176 average time/residue: 0.4441 time to fit residues: 100.1776 Evaluate side-chains 179 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.0050 chunk 107 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120107 restraints weight = 11411.606| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.20 r_work: 0.3167 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.133 Angle : 0.529 5.924 15439 Z= 0.288 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.037 1598 Dihedral : 23.758 153.649 2423 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.72 % Allowed : 11.28 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.31 (0.27), residues: 1067 helix: 1.07 (0.24), residues: 502 sheet: -1.39 (0.28), residues: 280 loop : 0.79 (0.43), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.007 0.002 PHE E 132 TYR 0.005 0.001 TYR F 36 ARG 0.008 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 428) hydrogen bonds : angle 4.13720 ( 1191) covalent geometry : bond 0.00306 (11086) covalent geometry : angle 0.52945 (15439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.113 Fit side-chains REVERT: B 68 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: C 17 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8098 (mt) REVERT: C 101 CYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6734 (m) REVERT: C 112 LYS cc_start: 0.8131 (mptt) cc_final: 0.7860 (tptp) REVERT: D 106 ASP cc_start: 0.7858 (t0) cc_final: 0.7626 (t0) REVERT: D 129 LYS cc_start: 0.7928 (tppt) cc_final: 0.7236 (tptt) REVERT: E 32 MET cc_start: 0.7742 (mmm) cc_final: 0.7322 (mmm) REVERT: E 100 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6991 (ttp80) REVERT: E 118 LYS cc_start: 0.8038 (mptt) cc_final: 0.7806 (mtpp) REVERT: E 123 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7390 (mtp85) REVERT: F 101 CYS cc_start: 0.6820 (m) cc_final: 0.6580 (m) REVERT: G 93 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7652 (pp) outliers start: 16 outliers final: 10 residues processed: 173 average time/residue: 0.3411 time to fit residues: 74.9142 Evaluate side-chains 179 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121757 restraints weight = 11429.949| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.22 r_work: 0.3173 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.127 Angle : 0.526 6.077 15439 Z= 0.287 Chirality : 0.037 0.133 1803 Planarity : 0.004 0.031 1598 Dihedral : 23.720 153.551 2423 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.50 % Allowed : 11.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.35 (0.27), residues: 1067 helix: 1.11 (0.24), residues: 502 sheet: -1.41 (0.28), residues: 280 loop : 0.82 (0.43), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.007 0.002 PHE E 132 TYR 0.005 0.001 TYR F 36 ARG 0.010 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 428) hydrogen bonds : angle 4.10117 ( 1191) covalent geometry : bond 0.00292 (11086) covalent geometry : angle 0.52595 (15439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9106.83 seconds wall clock time: 166 minutes 8.49 seconds (9968.49 seconds total)