Starting phenix.real_space_refine on Mon Sep 23 16:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/09_2024/7efc_31083.cif" } resolution = 1.7 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} bond proxies already assigned to first conformer: 867 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 40, 55 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 39} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: C, B, D Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O AHOH A5221 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5231 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 2.75, per 1000 atoms: 0.69 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 940 8.00 N 668 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 934.0 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 3.3% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 71 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY A 94 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 73 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP A 92 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP A 75 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 90 " --> pdb=" O TRP A 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 77 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER A 88 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP A 79 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 71 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 94 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 73 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP B 92 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP B 75 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 90 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 77 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER B 88 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP B 79 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 71 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 94 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 73 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP C 92 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP C 75 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 90 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL C 77 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER C 88 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP C 79 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR D 71 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY D 94 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 73 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP D 92 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP D 75 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR D 90 " --> pdb=" O TRP D 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 77 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER D 88 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP D 79 " --> pdb=" O ALA D 86 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 456 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: 1.12 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 548 1.29 - 1.42: 880 1.42 - 1.55: 2192 1.55 - 1.68: 316 1.68 - 1.81: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY B 94 " pdb=" O GLY B 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C ILE C 17 " pdb=" O ILE C 17 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.19e-02 7.06e+03 4.86e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 3396 2.66 - 5.33: 1508 5.33 - 7.99: 428 7.99 - 10.65: 44 10.65 - 13.32: 24 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.38 10.47 1.06e+00 8.90e-01 9.75e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 2008 16.54 - 33.08: 160 33.08 - 49.62: 20 49.62 - 66.16: 12 66.16 - 82.70: 12 Dihedral angle restraints: 2212 sinusoidal: 788 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASER A 52 " pdb=" C ASER A 52 " pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 2209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 412 0.080 - 0.160: 164 0.160 - 0.241: 20 0.241 - 0.321: 0 0.321 - 0.401: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL A 31 " pdb=" CA VAL A 31 " pdb=" CG1 VAL A 31 " pdb=" CG2 VAL A 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL C 31 " pdb=" CA VAL C 31 " pdb=" CG1 VAL C 31 " pdb=" CG2 VAL C 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL B 31 " pdb=" CA VAL B 31 " pdb=" CG1 VAL B 31 " pdb=" CG2 VAL B 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN C5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN C5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN C5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN C5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.262 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1438 2.94 - 3.92: 11594 3.92 - 4.90: 22880 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35914 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 3.040 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 3.040 nonbonded pdb=" O AASN C 49 " pdb=" OD1AASN C 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.057 3.040 ... (remaining 35909 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 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'B' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'C' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'D' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) } 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=0.50 max=1.00 mean=0.94 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: 0.290 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.032 0.090 3944 Z= 2.151 Angle : 3.162 13.316 5400 Z= 2.201 Chirality : 0.090 0.401 604 Planarity : 0.016 0.215 684 Dihedral : 14.879 82.705 1324 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 3.60 % 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: -0.84 (0.33), residues: 512 helix: None (None), residues: 0 sheet: 0.30 (0.29), residues: 244 loop : -1.41 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 92 HIS 0.001 0.000 HIS C 127 PHE 0.002 0.001 PHE D 130 TYR 0.002 0.001 TYR B 60 ARG 0.000 0.000 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8217 (m) cc_final: 0.7789 (p) REVERT: A 53 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: A 69 SER cc_start: 0.7845 (m) cc_final: 0.7634 (t) REVERT: A 103 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7435 (mtm-85) REVERT: B 27 SER cc_start: 0.8218 (m) cc_final: 0.7790 (p) REVERT: B 53 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7499 (ttp80) REVERT: B 69 SER cc_start: 0.7845 (m) cc_final: 0.7635 (t) REVERT: B 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7434 (mtm-85) REVERT: C 27 SER cc_start: 0.8215 (m) cc_final: 0.7788 (p) REVERT: C 53 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: C 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: C 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7433 (mtm-85) REVERT: D 27 SER cc_start: 0.8217 (m) cc_final: 0.7788 (p) REVERT: D 53 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7500 (ttp80) REVERT: D 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: D 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7435 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 1.1205 time to fit residues: 74.3874 Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 3944 Z= 0.587 Angle : 1.457 16.996 5400 Z= 0.814 Chirality : 0.075 0.458 604 Planarity : 0.014 0.100 684 Dihedral : 9.720 58.919 636 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.18 % Favored : 96.40 % Rotamer: Outliers : 1.61 % Allowed : 8.33 % Favored : 90.05 % 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: -1.59 (0.33), residues: 512 helix: -4.92 (0.29), residues: 24 sheet: -0.18 (0.27), residues: 264 loop : -1.64 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.008 TRP D 21 HIS 0.023 0.003 HIS C 87 PHE 0.107 0.019 PHE B 29 TYR 0.226 0.013 TYR B 43 ARG 0.047 0.004 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8269 (m) cc_final: 0.7956 (p) REVERT: A 53 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7558 (ttp80) REVERT: B 27 SER cc_start: 0.8234 (m) cc_final: 0.7920 (p) REVERT: C 27 SER cc_start: 0.8306 (m) cc_final: 0.7987 (p) REVERT: C 53 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7434 (ttp80) REVERT: D 27 SER cc_start: 0.8235 (m) cc_final: 0.7964 (p) REVERT: D 53 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7505 (ttp80) outliers start: 6 outliers final: 0 residues processed: 59 average time/residue: 1.2790 time to fit residues: 77.9908 Evaluate side-chains 48 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3944 Z= 0.199 Angle : 0.701 6.976 5400 Z= 0.377 Chirality : 0.044 0.149 604 Planarity : 0.004 0.025 684 Dihedral : 7.439 55.265 632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.61 % Rotamer: Outliers : 1.34 % Allowed : 6.45 % Favored : 92.20 % 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: -0.71 (0.34), residues: 512 helix: -5.08 (0.19), residues: 24 sheet: 0.02 (0.24), residues: 316 loop : -0.46 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.022 0.003 PHE A 29 TYR 0.016 0.002 TYR D 43 ARG 0.004 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8205 (m) cc_final: 0.7803 (p) REVERT: A 53 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7418 (ttm110) REVERT: B 27 SER cc_start: 0.8174 (m) cc_final: 0.7809 (p) REVERT: C 27 SER cc_start: 0.8237 (m) cc_final: 0.7884 (p) REVERT: C 53 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7350 (ttm110) REVERT: C 103 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7406 (ttp80) REVERT: D 27 SER cc_start: 0.8214 (m) cc_final: 0.7794 (p) REVERT: D 53 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7341 (ttm110) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 1.0843 time to fit residues: 77.6669 Evaluate side-chains 64 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3944 Z= 0.346 Angle : 0.794 8.774 5400 Z= 0.432 Chirality : 0.047 0.149 604 Planarity : 0.005 0.035 684 Dihedral : 8.253 42.701 632 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.81 % Allowed : 9.14 % Favored : 90.05 % 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: 0.48 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.31 (0.24), residues: 296 loop : 0.56 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 92 HIS 0.007 0.003 HIS C 87 PHE 0.027 0.004 PHE D 29 TYR 0.016 0.003 TYR D 22 ARG 0.007 0.002 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7463 (ttp80) REVERT: A 103 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7405 (ttm110) REVERT: C 53 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7448 (ttp80) REVERT: C 103 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7456 (ttm110) REVERT: D 53 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7544 (ttp80) REVERT: D 56 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (pp) REVERT: D 103 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7385 (ttm110) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 1.3522 time to fit residues: 73.9779 Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3944 Z= 0.215 Angle : 0.670 8.774 5400 Z= 0.358 Chirality : 0.043 0.154 604 Planarity : 0.003 0.018 684 Dihedral : 7.206 43.650 632 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.08 % Allowed : 8.87 % Favored : 90.05 % 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: -0.18 (0.33), residues: 512 helix: -5.21 (0.15), residues: 24 sheet: 0.46 (0.25), residues: 296 loop : -0.18 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 75 HIS 0.004 0.002 HIS C 87 PHE 0.017 0.003 PHE D 29 TYR 0.014 0.002 TYR C 22 ARG 0.003 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8228 (m) cc_final: 0.7736 (p) REVERT: A 53 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7546 (ttp80) REVERT: B 27 SER cc_start: 0.8226 (m) cc_final: 0.7750 (p) REVERT: C 27 SER cc_start: 0.8212 (m) cc_final: 0.7731 (p) REVERT: C 53 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7460 (ttp80) REVERT: C 103 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7407 (ttm110) REVERT: D 27 SER cc_start: 0.8213 (m) cc_final: 0.7741 (p) REVERT: D 53 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7480 (ttp80) REVERT: D 103 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7421 (ttm110) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 1.3241 time to fit residues: 76.6238 Evaluate side-chains 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3944 Z= 0.245 Angle : 0.681 9.041 5400 Z= 0.366 Chirality : 0.045 0.162 604 Planarity : 0.004 0.019 684 Dihedral : 7.368 44.829 632 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.61 % Allowed : 7.80 % Favored : 90.59 % 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: -0.13 (0.33), residues: 512 helix: -5.21 (0.15), residues: 24 sheet: 0.45 (0.25), residues: 296 loop : -0.06 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.004 0.002 HIS C 87 PHE 0.014 0.003 PHE D 29 TYR 0.009 0.002 TYR D 22 ARG 0.004 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7596 (ttp80) REVERT: C 53 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7544 (ttp80) REVERT: C 103 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7433 (ttm110) REVERT: D 53 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7434 (ttp80) outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 1.1965 time to fit residues: 69.2937 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3944 Z= 0.193 Angle : 0.648 8.862 5400 Z= 0.342 Chirality : 0.044 0.158 604 Planarity : 0.003 0.025 684 Dihedral : 6.987 46.248 632 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.34 % Allowed : 8.06 % Favored : 90.59 % 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: -0.19 (0.33), residues: 512 helix: -5.25 (0.15), residues: 24 sheet: 0.45 (0.25), residues: 304 loop : -0.19 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.009 0.002 PHE B 29 TYR 0.008 0.001 TYR B 83 ARG 0.006 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8198 (m) cc_final: 0.7769 (p) REVERT: A 53 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7546 (ttp80) REVERT: B 27 SER cc_start: 0.8198 (m) cc_final: 0.7765 (p) REVERT: C 27 SER cc_start: 0.8215 (m) cc_final: 0.7786 (p) REVERT: C 53 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7551 (ttp80) REVERT: C 103 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7389 (ttp80) REVERT: D 27 SER cc_start: 0.8209 (m) cc_final: 0.7780 (p) REVERT: D 53 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7535 (ttp80) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 1.2764 time to fit residues: 76.5846 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3944 Z= 0.269 Angle : 0.712 8.503 5400 Z= 0.380 Chirality : 0.046 0.164 604 Planarity : 0.004 0.030 684 Dihedral : 7.440 47.239 632 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.34 % Allowed : 8.60 % Favored : 90.05 % 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: -0.35 (0.33), residues: 512 helix: -5.25 (0.15), residues: 24 sheet: 0.32 (0.24), residues: 304 loop : -0.26 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.006 0.002 PHE D 29 TYR 0.009 0.002 TYR C 22 ARG 0.006 0.002 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7573 (ttp80) REVERT: C 53 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7510 (ttp80) REVERT: C 103 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7487 (ttm110) REVERT: D 53 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7478 (ttp80) REVERT: D 103 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7481 (ttm110) outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 1.3374 time to fit residues: 78.7056 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3944 Z= 0.349 Angle : 0.777 9.977 5400 Z= 0.417 Chirality : 0.049 0.194 604 Planarity : 0.005 0.030 684 Dihedral : 7.749 47.318 632 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.27 % Allowed : 9.41 % Favored : 90.32 % 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: 0.48 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.27 (0.24), residues: 304 loop : 0.63 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 92 HIS 0.007 0.003 HIS C 87 PHE 0.006 0.002 PHE A 29 TYR 0.009 0.002 TYR B 83 ARG 0.007 0.002 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7574 (ttp80) REVERT: C 53 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7523 (ttp80) REVERT: C 103 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7476 (ttm110) REVERT: D 53 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7529 (ttp80) REVERT: D 103 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7519 (ttm110) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 1.4090 time to fit residues: 77.0903 Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.188 Angle : 0.673 9.259 5400 Z= 0.349 Chirality : 0.044 0.157 604 Planarity : 0.003 0.021 684 Dihedral : 7.114 48.505 632 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 9.41 % Favored : 90.32 % 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: -0.30 (0.33), residues: 512 helix: -5.25 (0.15), residues: 24 sheet: 0.36 (0.25), residues: 304 loop : -0.26 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.003 0.001 HIS C 87 PHE 0.006 0.002 PHE B 29 TYR 0.008 0.001 TYR C 22 ARG 0.014 0.001 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8192 (m) cc_final: 0.7764 (p) REVERT: A 53 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7582 (ttp80) REVERT: B 27 SER cc_start: 0.8191 (m) cc_final: 0.7751 (p) REVERT: C 27 SER cc_start: 0.8189 (m) cc_final: 0.7755 (p) REVERT: C 53 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: C 103 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7384 (ttm110) REVERT: D 27 SER cc_start: 0.8172 (m) cc_final: 0.7742 (p) REVERT: D 53 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7515 (ttp80) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 1.3443 time to fit residues: 73.5387 Evaluate side-chains 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138732 restraints weight = 4034.050| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.24 r_work: 0.3674 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3944 Z= 0.266 Angle : 0.713 10.236 5400 Z= 0.380 Chirality : 0.046 0.159 604 Planarity : 0.004 0.023 684 Dihedral : 7.410 48.379 632 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.27 % Allowed : 9.68 % Favored : 90.05 % 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: -0.32 (0.33), residues: 512 helix: -5.25 (0.15), residues: 24 sheet: 0.34 (0.25), residues: 304 loop : -0.24 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.006 0.002 PHE D 29 TYR 0.010 0.002 TYR B 22 ARG 0.016 0.002 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.19 seconds wall clock time: 40 minutes 10.38 seconds (2410.38 seconds total)