Starting phenix.real_space_refine on Sun Dec 29 00:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqi_33397/12_2024/7xqi_33397.cif" } resolution = 3.7 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= 0.000 sd= 0.001 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 48 5.16 5 C 6396 2.51 5 N 1518 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.58, per 1000 atoms: 0.37 Number of scatterers: 9582 At special positions: 0 Unit cell: (102.608, 106, 103.456, 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 48 16.00 O 1620 8.00 N 1518 7.00 C 6396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 74.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 86 through 112 removed outlier: 3.728A pdb=" N GLU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 177 Processing helix chain 'B' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 86 through 112 removed outlier: 3.726A pdb=" N GLU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 177 Processing helix chain 'C' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 19 through 31 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 177 Processing helix chain 'D' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 177 Processing helix chain 'E' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.523A pdb=" N GLY F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 Processing helix chain 'F' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1911 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: 2.50 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2826 1.34 - 1.46: 2233 1.46 - 1.58: 4703 1.58 - 1.69: 6 1.69 - 1.81: 60 Bond restraints: 9828 Sorted by residual: bond pdb=" CA TYR E 17 " pdb=" CB TYR E 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.85e+00 bond pdb=" CA TYR F 17 " pdb=" CB TYR F 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.83e+00 bond pdb=" CA TYR B 17 " pdb=" CB TYR B 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.76e+00 bond pdb=" CA TYR A 17 " pdb=" CB TYR A 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.75e+00 bond pdb=" CA TYR C 17 " pdb=" CB TYR C 17 " ideal model delta sigma weight residual 1.531 1.598 -0.068 3.12e-02 1.03e+03 4.72e+00 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12951 1.77 - 3.54: 303 3.54 - 5.31: 24 5.31 - 7.08: 18 7.08 - 8.85: 12 Bond angle restraints: 13308 Sorted by residual: angle pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 ... (remaining 13303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 5063 14.30 - 28.60: 435 28.60 - 42.89: 163 42.89 - 57.19: 42 57.19 - 71.49: 36 Dihedral angle restraints: 5739 sinusoidal: 2289 harmonic: 3450 Sorted by residual: dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 793 0.028 - 0.056: 469 0.056 - 0.084: 182 0.084 - 0.113: 46 0.113 - 0.141: 34 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA ARG C 202 " pdb=" N ARG C 202 " pdb=" C ARG C 202 " pdb=" CB ARG C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ARG F 202 " pdb=" N ARG F 202 " pdb=" C ARG F 202 " pdb=" CB ARG F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VAL B 14 " pdb=" N VAL B 14 " pdb=" C VAL B 14 " pdb=" CB VAL B 14 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1521 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 167 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL C 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL C 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 167 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C VAL D 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL D 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 167 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C VAL A 167 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 167 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 168 " 0.009 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 78 2.60 - 3.18: 7583 3.18 - 3.75: 14376 3.75 - 4.33: 17550 4.33 - 4.90: 29760 Nonbonded interactions: 69347 Sorted by model distance: nonbonded pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 61 " pdb=" SG CYS C 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 61 " pdb=" SG CYS E 192 " model vdw 2.031 3.760 ... (remaining 69342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.860 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.120 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.006 0.069 9828 Z= 0.362 Angle : 0.716 8.849 13308 Z= 0.421 Chirality : 0.043 0.141 1524 Planarity : 0.005 0.028 1608 Dihedral : 14.155 71.487 3498 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.27 % Allowed : 7.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1152 helix: -1.10 (0.15), residues: 828 sheet: -0.68 (0.55), residues: 102 loop : -2.78 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 25 HIS 0.001 0.000 HIS F 95 PHE 0.011 0.001 PHE C 52 TYR 0.016 0.002 TYR C 17 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 100 MET cc_start: 0.8049 (tmm) cc_final: 0.7741 (tmm) REVERT: B 166 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9033 (mm-30) REVERT: B 231 VAL cc_start: 0.8127 (p) cc_final: 0.7762 (p) REVERT: C 166 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8978 (mm-30) REVERT: C 213 MET cc_start: 0.9159 (mmm) cc_final: 0.8923 (mmm) REVERT: F 166 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9030 (mm-30) outliers start: 24 outliers final: 7 residues processed: 204 average time/residue: 0.2452 time to fit residues: 69.1080 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 98 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9828 Z= 0.174 Angle : 0.544 5.612 13308 Z= 0.286 Chirality : 0.037 0.181 1524 Planarity : 0.003 0.024 1608 Dihedral : 4.899 40.968 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.46 % Allowed : 13.64 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.25), residues: 1152 helix: 1.33 (0.18), residues: 828 sheet: 2.76 (0.57), residues: 60 loop : -2.98 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 25 HIS 0.002 0.000 HIS A 194 PHE 0.008 0.001 PHE A 52 TYR 0.008 0.001 TYR A 177 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8133 (tmm) cc_final: 0.7789 (tmm) REVERT: A 148 ARG cc_start: 0.3999 (mtt-85) cc_final: 0.2899 (tpt170) REVERT: A 227 GLU cc_start: 0.8719 (tp30) cc_final: 0.8208 (tm-30) REVERT: B 47 ASP cc_start: 0.8306 (p0) cc_final: 0.8094 (p0) REVERT: C 47 ASP cc_start: 0.8199 (p0) cc_final: 0.7991 (p0) REVERT: C 166 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8659 (tp30) REVERT: C 187 CYS cc_start: 0.8143 (t) cc_final: 0.7756 (t) REVERT: C 213 MET cc_start: 0.9128 (mmm) cc_final: 0.8829 (mmm) REVERT: C 227 GLU cc_start: 0.8767 (tp30) cc_final: 0.8422 (tm-30) REVERT: D 166 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8691 (tp30) REVERT: D 187 CYS cc_start: 0.8097 (t) cc_final: 0.7590 (t) REVERT: D 227 GLU cc_start: 0.8848 (tp30) cc_final: 0.8377 (tm-30) REVERT: E 47 ASP cc_start: 0.8402 (p0) cc_final: 0.8179 (p0) REVERT: E 148 ARG cc_start: 0.4274 (mtt-85) cc_final: 0.3136 (tpt170) REVERT: E 187 CYS cc_start: 0.8335 (t) cc_final: 0.7889 (t) REVERT: F 47 ASP cc_start: 0.8251 (p0) cc_final: 0.8004 (p0) REVERT: F 148 ARG cc_start: 0.4567 (mtt-85) cc_final: 0.3379 (tpt170) REVERT: F 187 CYS cc_start: 0.8277 (t) cc_final: 0.7773 (t) REVERT: F 227 GLU cc_start: 0.8575 (tp30) cc_final: 0.8293 (tm-30) outliers start: 26 outliers final: 23 residues processed: 189 average time/residue: 0.1903 time to fit residues: 52.3230 Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9828 Z= 0.167 Angle : 0.523 7.132 13308 Z= 0.279 Chirality : 0.036 0.176 1524 Planarity : 0.004 0.028 1608 Dihedral : 4.710 39.892 1280 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.08 % Allowed : 17.23 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.68 (0.26), residues: 1152 helix: 2.11 (0.19), residues: 828 sheet: 2.80 (0.58), residues: 60 loop : -2.78 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 25 HIS 0.002 0.000 HIS A 74 PHE 0.020 0.001 PHE B 229 TYR 0.009 0.001 TYR A 177 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.080 Fit side-chains REVERT: A 47 ASP cc_start: 0.8285 (p0) cc_final: 0.8076 (p0) REVERT: A 148 ARG cc_start: 0.4144 (mtt-85) cc_final: 0.2966 (tpt170) REVERT: B 100 MET cc_start: 0.8252 (tmm) cc_final: 0.8043 (tmm) REVERT: B 101 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.8135 (tpp-160) REVERT: B 148 ARG cc_start: 0.4559 (mtt-85) cc_final: 0.3222 (tpt170) REVERT: B 166 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8718 (tp30) REVERT: C 47 ASP cc_start: 0.8201 (p0) cc_final: 0.7972 (p0) REVERT: C 148 ARG cc_start: 0.4511 (mtt-85) cc_final: 0.3459 (tpt170) REVERT: C 166 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8603 (tp30) REVERT: C 213 MET cc_start: 0.9127 (mmm) cc_final: 0.8881 (mmm) REVERT: C 227 GLU cc_start: 0.8802 (tp30) cc_final: 0.8379 (tm-30) REVERT: D 148 ARG cc_start: 0.3934 (mtt-85) cc_final: 0.2962 (tpt170) REVERT: E 47 ASP cc_start: 0.8304 (p0) cc_final: 0.8100 (p0) REVERT: E 148 ARG cc_start: 0.4452 (mtt-85) cc_final: 0.3168 (tpt170) REVERT: E 187 CYS cc_start: 0.8339 (t) cc_final: 0.7917 (t) REVERT: E 227 GLU cc_start: 0.8773 (tp30) cc_final: 0.8147 (tm-30) REVERT: F 148 ARG cc_start: 0.4534 (mtt-85) cc_final: 0.3399 (tpt170) REVERT: F 166 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8623 (tp30) outliers start: 22 outliers final: 15 residues processed: 189 average time/residue: 0.2007 time to fit residues: 53.7822 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0570 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 110 optimal weight: 0.0570 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9828 Z= 0.141 Angle : 0.516 5.560 13308 Z= 0.273 Chirality : 0.035 0.134 1524 Planarity : 0.003 0.030 1608 Dihedral : 3.902 37.487 1270 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.42 % Allowed : 21.31 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1152 helix: 2.47 (0.19), residues: 828 sheet: 1.73 (0.57), residues: 72 loop : -2.47 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 25 HIS 0.001 0.000 HIS E 74 PHE 0.022 0.001 PHE A 229 TYR 0.008 0.001 TYR B 185 ARG 0.004 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8192 (p0) cc_final: 0.7963 (p0) REVERT: A 100 MET cc_start: 0.8235 (tmm) cc_final: 0.7981 (tmm) REVERT: A 148 ARG cc_start: 0.4098 (mtt-85) cc_final: 0.3047 (tpt170) REVERT: B 100 MET cc_start: 0.8198 (tmm) cc_final: 0.7882 (tmm) REVERT: B 148 ARG cc_start: 0.4557 (mtt-85) cc_final: 0.3293 (tpt170) REVERT: B 166 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8636 (tp30) REVERT: B 187 CYS cc_start: 0.8295 (m) cc_final: 0.7927 (m) REVERT: B 213 MET cc_start: 0.9099 (mmm) cc_final: 0.8861 (mmm) REVERT: C 47 ASP cc_start: 0.8252 (p0) cc_final: 0.8012 (p0) REVERT: C 100 MET cc_start: 0.8301 (tmm) cc_final: 0.8033 (tmm) REVERT: C 148 ARG cc_start: 0.4408 (mtt-85) cc_final: 0.3434 (tpt170) REVERT: C 166 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8534 (tp30) REVERT: C 187 CYS cc_start: 0.8335 (m) cc_final: 0.7946 (m) REVERT: C 213 MET cc_start: 0.9150 (mmm) cc_final: 0.8936 (mmm) REVERT: D 101 ARG cc_start: 0.8843 (mmp80) cc_final: 0.8598 (tpp-160) REVERT: D 148 ARG cc_start: 0.3900 (mtt-85) cc_final: 0.3007 (tpt170) REVERT: D 227 GLU cc_start: 0.8817 (tp30) cc_final: 0.8383 (tm-30) REVERT: E 47 ASP cc_start: 0.8215 (p0) cc_final: 0.8004 (p0) REVERT: E 148 ARG cc_start: 0.4415 (mtt-85) cc_final: 0.3241 (tpt170) REVERT: E 213 MET cc_start: 0.9087 (mmm) cc_final: 0.8797 (mmm) REVERT: F 47 ASP cc_start: 0.7965 (p0) cc_final: 0.7680 (p0) REVERT: F 148 ARG cc_start: 0.4531 (mtt-85) cc_final: 0.3418 (tpt170) REVERT: F 166 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8540 (tp30) REVERT: F 187 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8043 (m) REVERT: F 213 MET cc_start: 0.9100 (mmm) cc_final: 0.8795 (mmm) outliers start: 15 outliers final: 13 residues processed: 187 average time/residue: 0.2026 time to fit residues: 53.6601 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9828 Z= 0.404 Angle : 0.683 6.482 13308 Z= 0.359 Chirality : 0.041 0.136 1524 Planarity : 0.004 0.029 1608 Dihedral : 4.064 20.112 1266 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.79 % Allowed : 21.12 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1152 helix: 2.39 (0.19), residues: 840 sheet: 1.33 (0.56), residues: 72 loop : -2.21 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 25 HIS 0.002 0.000 HIS A 74 PHE 0.015 0.001 PHE F 229 TYR 0.018 0.002 TYR C 66 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8212 (tmm) cc_final: 0.7882 (tmm) REVERT: B 31 ILE cc_start: 0.9368 (tp) cc_final: 0.9111 (tt) REVERT: B 100 MET cc_start: 0.8233 (tmm) cc_final: 0.7859 (tmm) REVERT: B 166 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8618 (tp30) REVERT: C 100 MET cc_start: 0.8381 (tmm) cc_final: 0.8119 (tmm) REVERT: C 213 MET cc_start: 0.9163 (mmm) cc_final: 0.8932 (mmm) REVERT: F 148 ARG cc_start: 0.4372 (mtt-85) cc_final: 0.3297 (tpt170) REVERT: F 187 CYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7982 (m) outliers start: 40 outliers final: 33 residues processed: 175 average time/residue: 0.1852 time to fit residues: 48.1469 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9828 Z= 0.171 Angle : 0.563 7.147 13308 Z= 0.295 Chirality : 0.036 0.115 1524 Planarity : 0.004 0.029 1608 Dihedral : 3.784 17.574 1266 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.61 % Allowed : 23.39 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1152 helix: 2.51 (0.19), residues: 834 sheet: 2.15 (0.57), residues: 60 loop : -2.49 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 25 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.001 PHE A 229 TYR 0.010 0.001 TYR A 177 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8184 (tmm) cc_final: 0.7865 (tmm) REVERT: A 148 ARG cc_start: 0.4135 (mtt-85) cc_final: 0.2998 (tpt170) REVERT: B 31 ILE cc_start: 0.9349 (tp) cc_final: 0.9096 (tt) REVERT: B 100 MET cc_start: 0.8264 (tmm) cc_final: 0.7883 (tmm) REVERT: B 148 ARG cc_start: 0.4617 (mtt-85) cc_final: 0.3245 (tpt170) REVERT: B 166 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8556 (tp30) REVERT: C 100 MET cc_start: 0.8399 (tmm) cc_final: 0.8133 (tmm) REVERT: C 148 ARG cc_start: 0.4449 (mtt-85) cc_final: 0.3422 (tpt170) REVERT: C 187 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8101 (m) REVERT: D 148 ARG cc_start: 0.3900 (mtt-85) cc_final: 0.2898 (tpt170) REVERT: E 100 MET cc_start: 0.8140 (tmm) cc_final: 0.7784 (tmm) REVERT: E 148 ARG cc_start: 0.4389 (mtt-85) cc_final: 0.3176 (tpt170) REVERT: F 148 ARG cc_start: 0.4449 (mtt-85) cc_final: 0.3406 (tpt170) REVERT: F 166 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8579 (tp30) REVERT: F 177 TYR cc_start: 0.8222 (m-80) cc_final: 0.8010 (m-80) REVERT: F 187 CYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8032 (m) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.2045 time to fit residues: 44.5844 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8352 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9828 Z= 0.151 Angle : 0.542 8.804 13308 Z= 0.283 Chirality : 0.035 0.115 1524 Planarity : 0.004 0.031 1608 Dihedral : 3.582 15.601 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 23.48 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.26), residues: 1152 helix: 2.66 (0.18), residues: 834 sheet: 2.35 (0.57), residues: 60 loop : -2.40 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 25 HIS 0.002 0.000 HIS D 194 PHE 0.012 0.001 PHE F 229 TYR 0.014 0.001 TYR C 177 ARG 0.003 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.235 Fit side-chains REVERT: A 148 ARG cc_start: 0.3915 (mtt-85) cc_final: 0.3038 (tpt170) REVERT: B 100 MET cc_start: 0.8254 (tmm) cc_final: 0.7805 (tmm) REVERT: B 148 ARG cc_start: 0.4319 (mtt-85) cc_final: 0.3214 (tpt170) REVERT: B 166 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8523 (tp30) REVERT: B 187 CYS cc_start: 0.8321 (m) cc_final: 0.8070 (m) REVERT: C 100 MET cc_start: 0.8404 (tmm) cc_final: 0.8057 (tmm) REVERT: C 148 ARG cc_start: 0.4597 (mtt-85) cc_final: 0.3451 (tpt170) REVERT: C 187 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8064 (m) REVERT: D 148 ARG cc_start: 0.3952 (mtt-85) cc_final: 0.3046 (tpt170) REVERT: E 148 ARG cc_start: 0.4392 (mtt-85) cc_final: 0.3273 (tpt170) REVERT: E 187 CYS cc_start: 0.8259 (m) cc_final: 0.7985 (m) REVERT: E 227 GLU cc_start: 0.8755 (tp30) cc_final: 0.8333 (tm-30) REVERT: F 148 ARG cc_start: 0.4370 (mtt-85) cc_final: 0.3401 (tpt170) REVERT: F 166 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8548 (tp30) REVERT: F 187 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8024 (m) outliers start: 18 outliers final: 15 residues processed: 161 average time/residue: 0.2067 time to fit residues: 46.8707 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8381 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9828 Z= 0.187 Angle : 0.575 9.318 13308 Z= 0.300 Chirality : 0.036 0.118 1524 Planarity : 0.004 0.032 1608 Dihedral : 3.591 16.835 1266 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.18 % Allowed : 23.58 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.26), residues: 1152 helix: 2.68 (0.18), residues: 834 sheet: 2.36 (0.57), residues: 60 loop : -2.42 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 25 HIS 0.004 0.000 HIS F 74 PHE 0.011 0.001 PHE A 229 TYR 0.014 0.001 TYR D 177 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.162 Fit side-chains REVERT: A 100 MET cc_start: 0.8153 (tmm) cc_final: 0.7793 (tmm) REVERT: A 148 ARG cc_start: 0.3943 (mtt-85) cc_final: 0.3133 (tpt170) REVERT: B 31 ILE cc_start: 0.9363 (tp) cc_final: 0.9124 (tt) REVERT: B 100 MET cc_start: 0.8091 (tmm) cc_final: 0.7679 (tmm) REVERT: B 148 ARG cc_start: 0.4301 (mtt-85) cc_final: 0.3210 (tpt170) REVERT: B 166 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8517 (tp30) REVERT: B 187 CYS cc_start: 0.8278 (m) cc_final: 0.8002 (m) REVERT: C 148 ARG cc_start: 0.4475 (mtt-85) cc_final: 0.3325 (tpt170) REVERT: C 187 CYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8092 (m) REVERT: D 148 ARG cc_start: 0.3755 (mtt-85) cc_final: 0.3038 (tpt170) REVERT: E 100 MET cc_start: 0.8096 (tmm) cc_final: 0.7741 (tmm) REVERT: E 148 ARG cc_start: 0.4464 (mtt-85) cc_final: 0.3218 (tpt170) REVERT: E 166 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8873 (mm-30) REVERT: E 187 CYS cc_start: 0.8314 (m) cc_final: 0.8002 (m) REVERT: F 148 ARG cc_start: 0.4423 (mtt-85) cc_final: 0.3415 (tpt170) REVERT: F 166 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8602 (tp30) REVERT: F 187 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8011 (m) outliers start: 23 outliers final: 21 residues processed: 163 average time/residue: 0.1978 time to fit residues: 46.0550 Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 0.0020 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 40.0000 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9828 Z= 0.153 Angle : 0.554 7.197 13308 Z= 0.289 Chirality : 0.035 0.116 1524 Planarity : 0.004 0.033 1608 Dihedral : 3.461 15.844 1266 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 23.67 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.26), residues: 1152 helix: 2.72 (0.18), residues: 834 sheet: 2.64 (0.57), residues: 60 loop : -2.43 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 25 HIS 0.001 0.000 HIS F 74 PHE 0.011 0.001 PHE F 229 TYR 0.017 0.001 TYR D 177 ARG 0.004 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.152 Fit side-chains REVERT: A 100 MET cc_start: 0.8112 (tmm) cc_final: 0.7737 (tmm) REVERT: A 148 ARG cc_start: 0.4002 (mtt-85) cc_final: 0.3145 (tpt170) REVERT: B 100 MET cc_start: 0.8100 (tmm) cc_final: 0.7674 (tmm) REVERT: B 148 ARG cc_start: 0.4438 (mtt-85) cc_final: 0.3319 (tpt170) REVERT: B 166 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8500 (tp30) REVERT: B 187 CYS cc_start: 0.8296 (m) cc_final: 0.8079 (m) REVERT: C 148 ARG cc_start: 0.4526 (mtt-85) cc_final: 0.3379 (tpt170) REVERT: C 187 CYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8119 (m) REVERT: C 227 GLU cc_start: 0.8887 (tp30) cc_final: 0.8327 (tm-30) REVERT: D 148 ARG cc_start: 0.3798 (mtt-85) cc_final: 0.3045 (tpt170) REVERT: E 148 ARG cc_start: 0.4412 (mtt-85) cc_final: 0.3280 (tpt170) REVERT: E 187 CYS cc_start: 0.8208 (m) cc_final: 0.7996 (m) REVERT: F 148 ARG cc_start: 0.4481 (mtt-85) cc_final: 0.3451 (tpt170) REVERT: F 166 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8541 (tp30) REVERT: F 187 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8059 (m) outliers start: 18 outliers final: 15 residues processed: 160 average time/residue: 0.1905 time to fit residues: 44.4361 Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 0.0770 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9828 Z= 0.307 Angle : 0.641 6.447 13308 Z= 0.337 Chirality : 0.039 0.127 1524 Planarity : 0.004 0.030 1608 Dihedral : 3.844 19.225 1266 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.80 % Allowed : 23.86 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.26), residues: 1152 helix: 2.64 (0.19), residues: 834 sheet: 2.25 (0.58), residues: 60 loop : -2.37 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 25 HIS 0.003 0.001 HIS F 74 PHE 0.011 0.001 PHE A 229 TYR 0.016 0.001 TYR D 177 ARG 0.004 0.000 ARG D 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.206 Fit side-chains REVERT: A 100 MET cc_start: 0.8162 (tmm) cc_final: 0.7789 (tmm) REVERT: A 148 ARG cc_start: 0.3746 (mtt-85) cc_final: 0.2927 (tpt170) REVERT: B 31 ILE cc_start: 0.9360 (tp) cc_final: 0.9127 (tt) REVERT: B 100 MET cc_start: 0.8140 (tmm) cc_final: 0.7626 (tmm) REVERT: B 148 ARG cc_start: 0.4389 (mtt-85) cc_final: 0.3150 (tpt170) REVERT: C 101 ARG cc_start: 0.9011 (tpp-160) cc_final: 0.8624 (tpp-160) REVERT: C 148 ARG cc_start: 0.4437 (mtt-85) cc_final: 0.3420 (tpt170) REVERT: C 187 CYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7981 (m) REVERT: D 100 MET cc_start: 0.8053 (tmm) cc_final: 0.7671 (tmm) REVERT: D 148 ARG cc_start: 0.3653 (mtt-85) cc_final: 0.2812 (tpt170) REVERT: E 100 MET cc_start: 0.8064 (tmm) cc_final: 0.7724 (tmm) REVERT: E 148 ARG cc_start: 0.4354 (mtt-85) cc_final: 0.3161 (tpt170) REVERT: E 166 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8923 (mm-30) REVERT: F 148 ARG cc_start: 0.4317 (mtt-85) cc_final: 0.3320 (tpt170) REVERT: F 166 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8703 (tp30) REVERT: F 187 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8045 (m) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 0.2028 time to fit residues: 39.8241 Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 187 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.100336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070033 restraints weight = 25810.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072448 restraints weight = 11971.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073805 restraints weight = 8129.693| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9828 Z= 0.177 Angle : 0.581 6.810 13308 Z= 0.305 Chirality : 0.036 0.126 1524 Planarity : 0.004 0.032 1608 Dihedral : 3.654 17.847 1266 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.61 % Allowed : 24.34 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.26), residues: 1152 helix: 2.64 (0.18), residues: 834 sheet: 2.27 (0.57), residues: 60 loop : -2.38 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 25 HIS 0.002 0.000 HIS F 74 PHE 0.011 0.001 PHE F 229 TYR 0.017 0.001 TYR D 177 ARG 0.004 0.000 ARG D 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.09 seconds wall clock time: 34 minutes 21.02 seconds (2061.02 seconds total)