Starting phenix.real_space_refine on Thu Mar 14 22:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqj_33398/03_2024/7xqj_33398.pdb" } resolution = 4.0 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 54 5.16 5 C 6642 2.51 5 N 1590 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Chain: "D" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Chain: "F" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Time building chain proxies: 5.54, per 1000 atoms: 0.56 Number of scatterers: 9960 At special positions: 0 Unit cell: (102.608, 104.304, 101.76, 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 54 16.00 O 1674 8.00 N 1590 7.00 C 6642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 73.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS A 13 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.523A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 Processing helix chain 'A' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 177 Processing helix chain 'B' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS C 13 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.545A pdb=" N GLY C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 177 Processing helix chain 'C' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.523A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 177 Processing helix chain 'D' and resid 202 through 238 removed outlier: 3.718A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 177 Processing helix chain 'E' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.545A pdb=" N GLY F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 177 Processing helix chain 'F' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.503A 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: 3.503A 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: 3.503A 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: 3.503A 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: 3.503A 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: 3.502A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1890 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: 2.72 Time building geometry restraints manager: 4.41 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: 2934 1.34 - 1.46: 2224 1.46 - 1.57: 4988 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 10218 Sorted by residual: bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.31e+00 bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 10213 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 192 106.51 - 113.38: 5716 113.38 - 120.24: 3977 120.24 - 127.11: 3819 127.11 - 133.98: 120 Bond angle restraints: 13824 Sorted by residual: angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" C GLU B 42 " ideal model delta sigma weight residual 112.90 107.89 5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N GLU A 42 " pdb=" CA GLU A 42 " pdb=" C GLU A 42 " ideal model delta sigma weight residual 112.90 107.90 5.00 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" C GLU D 42 " ideal model delta sigma weight residual 112.90 107.91 4.99 1.31e+00 5.83e-01 1.45e+01 angle pdb=" N GLU C 42 " pdb=" CA GLU C 42 " pdb=" C GLU C 42 " ideal model delta sigma weight residual 112.90 107.93 4.97 1.31e+00 5.83e-01 1.44e+01 angle pdb=" N GLU F 42 " pdb=" CA GLU F 42 " pdb=" C GLU F 42 " ideal model delta sigma weight residual 112.90 107.93 4.97 1.31e+00 5.83e-01 1.44e+01 ... (remaining 13819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 5149 13.83 - 27.65: 479 27.65 - 41.48: 210 41.48 - 55.30: 120 55.30 - 69.13: 54 Dihedral angle restraints: 6012 sinusoidal: 2430 harmonic: 3582 Sorted by residual: dihedral pdb=" CA PRO B 193 " pdb=" C PRO B 193 " pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+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 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PRO A 193 " pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta harmonic sigma weight residual 180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 998 0.035 - 0.071: 373 0.071 - 0.106: 157 0.106 - 0.141: 32 0.141 - 0.177: 12 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ALA E 6 " pdb=" N ALA E 6 " pdb=" C ALA E 6 " pdb=" CB ALA E 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ALA C 6 " pdb=" N ALA C 6 " pdb=" C ALA C 6 " pdb=" CB ALA C 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ALA F 6 " pdb=" N ALA F 6 " pdb=" C ALA F 6 " pdb=" CB ALA F 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 1569 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 87 " 0.035 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 88 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 87 " 0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO F 88 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 87 " 0.035 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO E 88 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 88 " 0.030 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3939 2.90 - 3.40: 9991 3.40 - 3.90: 16156 3.90 - 4.40: 15725 4.40 - 4.90: 27759 Nonbonded interactions: 73570 Sorted by model distance: nonbonded pdb=" O ALA C 40 " pdb=" OG SER C 43 " model vdw 2.401 2.440 nonbonded pdb=" O ALA D 40 " pdb=" OG SER D 43 " model vdw 2.402 2.440 nonbonded pdb=" O ALA A 40 " pdb=" OG SER A 43 " model vdw 2.402 2.440 nonbonded pdb=" O ALA F 40 " pdb=" OG SER F 43 " model vdw 2.402 2.440 nonbonded pdb=" O ALA E 40 " pdb=" OG SER E 43 " model vdw 2.402 2.440 ... (remaining 73565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.090 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: 4.050 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 28.840 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.007 0.049 10218 Z= 0.413 Angle : 0.838 8.257 13824 Z= 0.488 Chirality : 0.045 0.177 1572 Planarity : 0.007 0.052 1662 Dihedral : 15.982 69.127 3642 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.01 % Allowed : 11.48 % Favored : 82.51 % 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: -2.82 (0.20), residues: 1200 helix: -1.68 (0.14), residues: 822 sheet: 2.82 (0.55), residues: 60 loop : -2.92 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 25 HIS 0.003 0.001 HIS E 74 PHE 0.011 0.002 PHE C 97 TYR 0.008 0.001 TYR D 92 ARG 0.004 0.001 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 259 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7359 (p90) REVERT: A 47 ASP cc_start: 0.8821 (p0) cc_final: 0.8566 (p0) REVERT: A 100 MET cc_start: 0.9574 (ttp) cc_final: 0.8899 (tmm) REVERT: A 101 ARG cc_start: 0.9461 (ttm170) cc_final: 0.9100 (ttp-110) REVERT: A 213 MET cc_start: 0.9231 (mmm) cc_final: 0.8886 (mmp) REVERT: A 224 ASN cc_start: 0.8962 (m110) cc_final: 0.8571 (m110) REVERT: A 227 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9124 (tm-30) REVERT: B 17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7252 (p90) REVERT: B 100 MET cc_start: 0.9586 (ttp) cc_final: 0.9010 (ppp) REVERT: B 101 ARG cc_start: 0.9385 (ttm170) cc_final: 0.9025 (ttp-110) REVERT: B 104 GLU cc_start: 0.9417 (tp30) cc_final: 0.9077 (mm-30) REVERT: B 224 ASN cc_start: 0.8974 (m110) cc_final: 0.8561 (m110) REVERT: B 227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9010 (tm-30) REVERT: C 17 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 100 MET cc_start: 0.9549 (ttp) cc_final: 0.9031 (ppp) REVERT: C 101 ARG cc_start: 0.9407 (ttm170) cc_final: 0.9029 (ttp-110) REVERT: C 227 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9242 (tm-30) REVERT: D 17 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7089 (p90) REVERT: D 47 ASP cc_start: 0.8790 (p0) cc_final: 0.8497 (p0) REVERT: D 81 GLN cc_start: 0.9439 (tt0) cc_final: 0.9198 (tt0) REVERT: D 100 MET cc_start: 0.9557 (ttp) cc_final: 0.9050 (tmm) REVERT: D 101 ARG cc_start: 0.9439 (ttm170) cc_final: 0.9220 (ttp-110) REVERT: D 104 GLU cc_start: 0.9472 (tp30) cc_final: 0.9245 (mm-30) REVERT: D 213 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mmp) REVERT: D 224 ASN cc_start: 0.9021 (m110) cc_final: 0.8658 (m110) REVERT: D 227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9191 (tm-30) REVERT: E 17 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7235 (p90) REVERT: E 100 MET cc_start: 0.9585 (ttp) cc_final: 0.9013 (ppp) REVERT: E 101 ARG cc_start: 0.9386 (ttm170) cc_final: 0.9019 (ttp-110) REVERT: E 104 GLU cc_start: 0.9413 (tp30) cc_final: 0.9076 (mm-30) REVERT: E 224 ASN cc_start: 0.8972 (m110) cc_final: 0.8559 (m110) REVERT: E 227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9021 (tm-30) REVERT: F 17 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7395 (p90) REVERT: F 100 MET cc_start: 0.9553 (ttp) cc_final: 0.9040 (ppp) REVERT: F 101 ARG cc_start: 0.9408 (ttm170) cc_final: 0.9036 (ttp-110) REVERT: F 227 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9238 (tm-30) outliers start: 66 outliers final: 13 residues processed: 307 average time/residue: 0.2020 time to fit residues: 86.5306 Evaluate side-chains 204 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 74 HIS A 224 ASN B 74 HIS B 81 GLN B 224 ASN C 74 HIS D 15 GLN D 74 HIS D 224 ASN E 74 HIS E 81 GLN E 224 ASN F 74 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10218 Z= 0.203 Angle : 0.713 8.085 13824 Z= 0.358 Chirality : 0.039 0.157 1572 Planarity : 0.004 0.034 1662 Dihedral : 7.761 55.222 1352 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.83 % Allowed : 18.12 % Favored : 75.05 % 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: -0.40 (0.25), residues: 1200 helix: 0.37 (0.18), residues: 852 sheet: 2.83 (0.59), residues: 60 loop : -2.79 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 25 HIS 0.002 0.001 HIS C 74 PHE 0.014 0.001 PHE C 30 TYR 0.010 0.001 TYR A 92 ARG 0.005 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 191 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7518 (p90) REVERT: A 100 MET cc_start: 0.9425 (ttp) cc_final: 0.9128 (ppp) REVERT: A 101 ARG cc_start: 0.9454 (ttm170) cc_final: 0.9074 (ttp80) REVERT: A 213 MET cc_start: 0.9182 (mmm) cc_final: 0.8863 (mmp) REVERT: A 224 ASN cc_start: 0.8804 (m-40) cc_final: 0.8441 (m110) REVERT: A 227 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9129 (tm-30) REVERT: B 17 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7156 (p90) REVERT: B 100 MET cc_start: 0.9408 (ttp) cc_final: 0.9090 (ppp) REVERT: B 101 ARG cc_start: 0.9379 (ttm170) cc_final: 0.9134 (ttp80) REVERT: B 224 ASN cc_start: 0.8862 (m-40) cc_final: 0.8439 (m110) REVERT: B 227 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9029 (tm-30) REVERT: C 17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7253 (p90) REVERT: C 100 MET cc_start: 0.9361 (ttp) cc_final: 0.9016 (ppp) REVERT: C 101 ARG cc_start: 0.9413 (ttm170) cc_final: 0.9138 (ttp80) REVERT: C 227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9214 (tm-30) REVERT: D 17 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7000 (p90) REVERT: D 42 GLU cc_start: 0.8420 (pp20) cc_final: 0.8203 (mt-10) REVERT: D 100 MET cc_start: 0.9413 (ttp) cc_final: 0.9173 (ppp) REVERT: D 101 ARG cc_start: 0.9441 (ttm170) cc_final: 0.9158 (ttp80) REVERT: D 213 MET cc_start: 0.9254 (mmm) cc_final: 0.8994 (mmp) REVERT: D 224 ASN cc_start: 0.8845 (m-40) cc_final: 0.8488 (m110) REVERT: D 227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9179 (tm-30) REVERT: E 17 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7249 (p90) REVERT: E 101 ARG cc_start: 0.9381 (ttm170) cc_final: 0.9010 (ttp80) REVERT: E 197 ASP cc_start: 0.8807 (m-30) cc_final: 0.8606 (t0) REVERT: E 224 ASN cc_start: 0.8867 (m-40) cc_final: 0.8441 (m110) REVERT: E 227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9018 (tm-30) REVERT: F 17 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7270 (p90) REVERT: F 100 MET cc_start: 0.9373 (ttp) cc_final: 0.9012 (ppp) REVERT: F 101 ARG cc_start: 0.9411 (ttm170) cc_final: 0.9136 (ttp80) REVERT: F 227 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9218 (tm-30) outliers start: 75 outliers final: 28 residues processed: 249 average time/residue: 0.1821 time to fit residues: 66.4548 Evaluate side-chains 202 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 0.0670 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 81 GLN E 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10218 Z= 0.202 Angle : 0.668 8.071 13824 Z= 0.342 Chirality : 0.038 0.157 1572 Planarity : 0.004 0.036 1662 Dihedral : 7.491 55.687 1352 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.10 % Allowed : 21.04 % Favored : 73.86 % 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: 0.52 (0.25), residues: 1200 helix: 1.20 (0.18), residues: 822 sheet: 2.50 (0.58), residues: 60 loop : -2.46 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 25 HIS 0.004 0.001 HIS A 74 PHE 0.016 0.001 PHE B 30 TYR 0.018 0.001 TYR B 66 ARG 0.002 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 187 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7408 (p90) REVERT: A 48 GLU cc_start: 0.9204 (tp30) cc_final: 0.8440 (tm-30) REVERT: A 100 MET cc_start: 0.9420 (ttp) cc_final: 0.9133 (ppp) REVERT: A 101 ARG cc_start: 0.9456 (ttm170) cc_final: 0.9086 (ttp-110) REVERT: A 213 MET cc_start: 0.9165 (mmm) cc_final: 0.8852 (mmp) REVERT: A 224 ASN cc_start: 0.8777 (m-40) cc_final: 0.8402 (m110) REVERT: A 227 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9131 (tm-30) REVERT: B 17 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7283 (p90) REVERT: B 101 ARG cc_start: 0.9384 (ttm170) cc_final: 0.8948 (ttp-110) REVERT: B 224 ASN cc_start: 0.8861 (m-40) cc_final: 0.8422 (m110) REVERT: B 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9021 (tm-30) REVERT: C 17 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7236 (p90) REVERT: C 42 GLU cc_start: 0.9084 (tp30) cc_final: 0.8761 (tp30) REVERT: C 48 GLU cc_start: 0.9190 (tp30) cc_final: 0.8352 (tm-30) REVERT: C 49 GLN cc_start: 0.8765 (tt0) cc_final: 0.8536 (tp40) REVERT: C 100 MET cc_start: 0.9286 (ttp) cc_final: 0.9063 (ppp) REVERT: C 101 ARG cc_start: 0.9425 (ttm170) cc_final: 0.9044 (ttp-110) REVERT: C 227 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9212 (tm-30) REVERT: D 17 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7162 (p90) REVERT: D 48 GLU cc_start: 0.9117 (tp30) cc_final: 0.8565 (tm-30) REVERT: D 100 MET cc_start: 0.9403 (ttp) cc_final: 0.9176 (ppp) REVERT: D 101 ARG cc_start: 0.9436 (ttm170) cc_final: 0.9148 (ttp80) REVERT: D 213 MET cc_start: 0.9246 (mmm) cc_final: 0.8982 (mmp) REVERT: D 224 ASN cc_start: 0.8831 (m-40) cc_final: 0.8463 (m110) REVERT: D 227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9182 (tm-30) REVERT: E 17 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7280 (p90) REVERT: E 48 GLU cc_start: 0.9270 (tp30) cc_final: 0.8532 (tm-30) REVERT: E 101 ARG cc_start: 0.9387 (ttm170) cc_final: 0.8942 (ttp-110) REVERT: E 197 ASP cc_start: 0.8835 (m-30) cc_final: 0.8583 (t0) REVERT: E 224 ASN cc_start: 0.8860 (m-40) cc_final: 0.8435 (m110) REVERT: E 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9017 (tm-30) REVERT: F 17 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7259 (p90) REVERT: F 42 GLU cc_start: 0.9103 (tp30) cc_final: 0.8770 (tp30) REVERT: F 48 GLU cc_start: 0.9197 (tp30) cc_final: 0.8329 (tm-30) REVERT: F 49 GLN cc_start: 0.8794 (tt0) cc_final: 0.8528 (tp40) REVERT: F 100 MET cc_start: 0.9284 (ttp) cc_final: 0.9059 (ppp) REVERT: F 101 ARG cc_start: 0.9425 (ttm170) cc_final: 0.9047 (ttp-110) REVERT: F 227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9203 (tm-30) outliers start: 56 outliers final: 28 residues processed: 226 average time/residue: 0.1861 time to fit residues: 61.4880 Evaluate side-chains 201 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10218 Z= 0.239 Angle : 0.643 7.639 13824 Z= 0.335 Chirality : 0.038 0.146 1572 Planarity : 0.004 0.040 1662 Dihedral : 6.736 53.436 1340 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.38 % Allowed : 20.49 % Favored : 73.13 % 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: 0.80 (0.25), residues: 1200 helix: 1.43 (0.19), residues: 822 sheet: 1.63 (0.62), residues: 66 loop : -2.22 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 25 HIS 0.003 0.001 HIS A 74 PHE 0.013 0.001 PHE B 30 TYR 0.017 0.001 TYR A 66 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7531 (p90) REVERT: A 48 GLU cc_start: 0.9284 (tp30) cc_final: 0.8717 (tm-30) REVERT: A 100 MET cc_start: 0.9391 (ttp) cc_final: 0.9133 (ppp) REVERT: A 101 ARG cc_start: 0.9459 (ttm170) cc_final: 0.9094 (ttp-110) REVERT: A 213 MET cc_start: 0.9171 (mmm) cc_final: 0.8881 (mmp) REVERT: A 224 ASN cc_start: 0.8779 (m-40) cc_final: 0.8401 (m110) REVERT: A 227 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9138 (tm-30) REVERT: B 17 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7475 (p90) REVERT: B 48 GLU cc_start: 0.9273 (tp30) cc_final: 0.8594 (tm-30) REVERT: B 101 ARG cc_start: 0.9392 (ttm170) cc_final: 0.9067 (ttp-110) REVERT: B 213 MET cc_start: 0.9221 (mmm) cc_final: 0.9008 (mmp) REVERT: B 224 ASN cc_start: 0.8880 (m-40) cc_final: 0.8447 (m110) REVERT: B 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9030 (tm-30) REVERT: C 17 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7541 (p90) REVERT: C 48 GLU cc_start: 0.9168 (tp30) cc_final: 0.8548 (tm-30) REVERT: C 100 MET cc_start: 0.9330 (ttp) cc_final: 0.9076 (ppp) REVERT: C 101 ARG cc_start: 0.9424 (ttm170) cc_final: 0.9049 (ttp-110) REVERT: C 227 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9230 (tm-30) REVERT: D 17 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.6814 (p90) REVERT: D 48 GLU cc_start: 0.9099 (tp30) cc_final: 0.8334 (tm-30) REVERT: D 49 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8742 (tp40) REVERT: D 100 MET cc_start: 0.9400 (ttp) cc_final: 0.9183 (ppp) REVERT: D 101 ARG cc_start: 0.9433 (ttm170) cc_final: 0.9161 (ttp-110) REVERT: D 213 MET cc_start: 0.9236 (mmm) cc_final: 0.8979 (mmp) REVERT: D 224 ASN cc_start: 0.8867 (m-40) cc_final: 0.8483 (m110) REVERT: D 227 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9188 (tm-30) REVERT: E 17 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7483 (p90) REVERT: E 48 GLU cc_start: 0.9215 (tp30) cc_final: 0.8598 (tm-30) REVERT: E 101 ARG cc_start: 0.9403 (ttm170) cc_final: 0.9066 (ttp-110) REVERT: E 197 ASP cc_start: 0.8861 (m-30) cc_final: 0.8572 (t0) REVERT: E 213 MET cc_start: 0.9220 (mmm) cc_final: 0.9001 (mmp) REVERT: E 224 ASN cc_start: 0.8877 (m-40) cc_final: 0.8447 (m110) REVERT: E 227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9027 (tm-30) REVERT: F 17 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7526 (p90) REVERT: F 100 MET cc_start: 0.9326 (ttp) cc_final: 0.9074 (ppp) REVERT: F 101 ARG cc_start: 0.9423 (ttm170) cc_final: 0.9042 (ttp-110) REVERT: F 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9219 (tm-30) outliers start: 70 outliers final: 34 residues processed: 225 average time/residue: 0.1994 time to fit residues: 63.8641 Evaluate side-chains 202 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0770 chunk 65 optimal weight: 0.0370 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.0040 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10218 Z= 0.182 Angle : 0.658 6.077 13824 Z= 0.336 Chirality : 0.039 0.182 1572 Planarity : 0.004 0.034 1662 Dihedral : 6.414 53.209 1334 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.46 % Allowed : 22.50 % Favored : 73.04 % 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: 1.00 (0.25), residues: 1200 helix: 1.60 (0.19), residues: 822 sheet: 1.48 (0.61), residues: 66 loop : -2.18 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 25 HIS 0.002 0.001 HIS A 74 PHE 0.013 0.001 PHE B 30 TYR 0.016 0.001 TYR B 92 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7407 (p90) REVERT: A 48 GLU cc_start: 0.9208 (tp30) cc_final: 0.8721 (tm-30) REVERT: A 100 MET cc_start: 0.9400 (ttp) cc_final: 0.9149 (ppp) REVERT: A 101 ARG cc_start: 0.9458 (ttm170) cc_final: 0.9078 (ttp-110) REVERT: A 213 MET cc_start: 0.9148 (mmm) cc_final: 0.8840 (mmp) REVERT: A 227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9108 (tm-30) REVERT: B 17 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7470 (p90) REVERT: B 48 GLU cc_start: 0.9220 (tp30) cc_final: 0.8714 (tm-30) REVERT: B 101 ARG cc_start: 0.9519 (ttm170) cc_final: 0.9054 (ttp-110) REVERT: B 224 ASN cc_start: 0.8815 (m-40) cc_final: 0.8594 (m110) REVERT: B 227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9009 (tm-30) REVERT: C 17 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7426 (p90) REVERT: C 100 MET cc_start: 0.9341 (ttp) cc_final: 0.9103 (ppp) REVERT: C 101 ARG cc_start: 0.9418 (ttm170) cc_final: 0.9039 (ttp-110) REVERT: C 227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9215 (tm-30) REVERT: D 17 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7083 (p90) REVERT: D 48 GLU cc_start: 0.9009 (tp30) cc_final: 0.8381 (tm-30) REVERT: D 49 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8840 (tp40) REVERT: D 101 ARG cc_start: 0.9428 (ttm170) cc_final: 0.9156 (ttp-110) REVERT: D 213 MET cc_start: 0.9220 (mmm) cc_final: 0.8966 (mmp) REVERT: D 224 ASN cc_start: 0.8828 (m-40) cc_final: 0.8449 (m110) REVERT: D 227 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9160 (tm-30) REVERT: E 17 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7458 (p90) REVERT: E 48 GLU cc_start: 0.9125 (tp30) cc_final: 0.8620 (tm-30) REVERT: E 72 ILE cc_start: 0.9523 (pt) cc_final: 0.9319 (tt) REVERT: E 101 ARG cc_start: 0.9520 (ttm170) cc_final: 0.9049 (ttp-110) REVERT: E 197 ASP cc_start: 0.8861 (m-30) cc_final: 0.8594 (t0) REVERT: E 224 ASN cc_start: 0.8827 (m-40) cc_final: 0.8604 (m110) REVERT: E 227 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9016 (tm-30) REVERT: F 17 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7434 (p90) REVERT: F 100 MET cc_start: 0.9335 (ttp) cc_final: 0.9100 (ppp) REVERT: F 101 ARG cc_start: 0.9408 (ttm170) cc_final: 0.9038 (ttp-110) REVERT: F 227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9206 (tm-30) outliers start: 49 outliers final: 29 residues processed: 219 average time/residue: 0.1827 time to fit residues: 58.8306 Evaluate side-chains 204 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 0.0370 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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: 0.8407 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10218 Z= 0.173 Angle : 0.659 8.064 13824 Z= 0.337 Chirality : 0.039 0.178 1572 Planarity : 0.004 0.034 1662 Dihedral : 6.166 54.202 1332 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.10 % Allowed : 24.50 % Favored : 71.40 % 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: 1.14 (0.25), residues: 1200 helix: 1.67 (0.19), residues: 822 sheet: 1.91 (0.67), residues: 66 loop : -2.07 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 25 HIS 0.002 0.000 HIS A 74 PHE 0.011 0.001 PHE B 30 TYR 0.015 0.001 TYR D 92 ARG 0.002 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7292 (p90) REVERT: A 48 GLU cc_start: 0.9181 (tp30) cc_final: 0.8722 (tm-30) REVERT: A 100 MET cc_start: 0.9398 (ttp) cc_final: 0.9158 (ppp) REVERT: A 101 ARG cc_start: 0.9454 (ttm170) cc_final: 0.9074 (ttp-110) REVERT: A 213 MET cc_start: 0.9153 (mmm) cc_final: 0.8850 (mmp) REVERT: A 227 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9153 (tm-30) REVERT: B 17 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7257 (p90) REVERT: B 48 GLU cc_start: 0.9192 (tp30) cc_final: 0.8775 (tm-30) REVERT: B 101 ARG cc_start: 0.9521 (ttm170) cc_final: 0.9061 (ttp-110) REVERT: B 213 MET cc_start: 0.9175 (mmm) cc_final: 0.8966 (mmp) REVERT: B 227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.8995 (tm-30) REVERT: C 17 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7426 (p90) REVERT: C 100 MET cc_start: 0.9349 (ttp) cc_final: 0.9109 (ppp) REVERT: C 101 ARG cc_start: 0.9419 (ttm170) cc_final: 0.9041 (ttp-110) REVERT: C 227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9220 (tm-30) REVERT: D 17 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.6960 (p90) REVERT: D 101 ARG cc_start: 0.9589 (ttm170) cc_final: 0.9148 (ttp-110) REVERT: D 213 MET cc_start: 0.9222 (mmm) cc_final: 0.8969 (mmp) REVERT: D 224 ASN cc_start: 0.8807 (m-40) cc_final: 0.8400 (m110) REVERT: D 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9159 (tm-30) REVERT: E 17 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7257 (p90) REVERT: E 48 GLU cc_start: 0.9088 (tp30) cc_final: 0.8659 (tm-30) REVERT: E 101 ARG cc_start: 0.9524 (ttm170) cc_final: 0.9062 (ttp-110) REVERT: E 197 ASP cc_start: 0.8944 (m-30) cc_final: 0.8637 (t0) REVERT: E 227 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9005 (tm-30) REVERT: F 17 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7436 (p90) REVERT: F 100 MET cc_start: 0.9343 (ttp) cc_final: 0.9109 (ppp) REVERT: F 101 ARG cc_start: 0.9413 (ttm170) cc_final: 0.9041 (ttp-110) REVERT: F 227 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9206 (tm-30) outliers start: 45 outliers final: 27 residues processed: 212 average time/residue: 0.1902 time to fit residues: 59.1821 Evaluate side-chains 203 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10218 Z= 0.222 Angle : 0.671 9.638 13824 Z= 0.345 Chirality : 0.039 0.149 1572 Planarity : 0.004 0.038 1662 Dihedral : 6.056 55.171 1330 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.01 % Allowed : 26.59 % Favored : 68.40 % 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: 1.20 (0.25), residues: 1200 helix: 1.64 (0.19), residues: 828 sheet: 1.87 (0.67), residues: 66 loop : -1.89 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 25 HIS 0.005 0.001 HIS D 74 PHE 0.026 0.001 PHE B 30 TYR 0.017 0.001 TYR D 92 ARG 0.002 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7301 (p90) REVERT: A 48 GLU cc_start: 0.9200 (tp30) cc_final: 0.8684 (tm-30) REVERT: A 100 MET cc_start: 0.9395 (ttp) cc_final: 0.9166 (ppp) REVERT: A 101 ARG cc_start: 0.9455 (ttm170) cc_final: 0.9074 (ttp-110) REVERT: A 213 MET cc_start: 0.9186 (mmm) cc_final: 0.8902 (mmp) REVERT: A 227 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9171 (tm-30) REVERT: B 17 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7318 (p90) REVERT: B 48 GLU cc_start: 0.9170 (tp30) cc_final: 0.8776 (tm-30) REVERT: B 81 GLN cc_start: 0.9499 (tt0) cc_final: 0.9247 (tp-100) REVERT: B 101 ARG cc_start: 0.9529 (ttm170) cc_final: 0.9079 (ttp-110) REVERT: B 213 MET cc_start: 0.9199 (mmm) cc_final: 0.8909 (mmp) REVERT: B 227 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9077 (tm-30) REVERT: C 17 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7436 (p90) REVERT: C 100 MET cc_start: 0.9340 (ttp) cc_final: 0.9105 (ppp) REVERT: C 101 ARG cc_start: 0.9414 (ttm170) cc_final: 0.9048 (ttp-110) REVERT: C 227 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9221 (tm-30) REVERT: D 17 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7106 (p90) REVERT: D 101 ARG cc_start: 0.9606 (ttm170) cc_final: 0.9169 (ttp-110) REVERT: D 213 MET cc_start: 0.9218 (mmm) cc_final: 0.8982 (mmp) REVERT: D 224 ASN cc_start: 0.8832 (m-40) cc_final: 0.8424 (m110) REVERT: D 227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9167 (tm-30) REVERT: E 17 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7323 (p90) REVERT: E 48 GLU cc_start: 0.9095 (tp30) cc_final: 0.8664 (tm-30) REVERT: E 81 GLN cc_start: 0.9503 (tt0) cc_final: 0.9254 (tp-100) REVERT: E 101 ARG cc_start: 0.9533 (ttm170) cc_final: 0.9077 (ttp-110) REVERT: E 197 ASP cc_start: 0.8938 (m-30) cc_final: 0.8590 (t0) REVERT: E 213 MET cc_start: 0.9201 (mmm) cc_final: 0.8904 (mmp) REVERT: E 227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9046 (tm-30) REVERT: F 17 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7448 (p90) REVERT: F 100 MET cc_start: 0.9343 (ttp) cc_final: 0.9111 (ppp) REVERT: F 101 ARG cc_start: 0.9411 (ttm170) cc_final: 0.9045 (ttp-110) REVERT: F 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9202 (tm-30) outliers start: 55 outliers final: 22 residues processed: 215 average time/residue: 0.1862 time to fit residues: 58.2919 Evaluate side-chains 198 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.0670 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 0.0870 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10218 Z= 0.173 Angle : 0.687 8.408 13824 Z= 0.348 Chirality : 0.039 0.149 1572 Planarity : 0.004 0.035 1662 Dihedral : 5.590 50.556 1326 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 28.14 % Favored : 68.85 % 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: 1.21 (0.25), residues: 1200 helix: 1.63 (0.19), residues: 828 sheet: 1.96 (0.68), residues: 66 loop : -1.83 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 25 HIS 0.002 0.001 HIS B 74 PHE 0.028 0.001 PHE E 30 TYR 0.016 0.001 TYR A 92 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7156 (p90) REVERT: A 42 GLU cc_start: 0.8313 (pp20) cc_final: 0.8008 (pp20) REVERT: A 48 GLU cc_start: 0.9138 (tp30) cc_final: 0.8716 (tm-30) REVERT: A 100 MET cc_start: 0.9395 (ttp) cc_final: 0.9172 (ppp) REVERT: A 101 ARG cc_start: 0.9447 (ttm170) cc_final: 0.9091 (ptm-80) REVERT: A 213 MET cc_start: 0.9163 (mmm) cc_final: 0.8883 (mmp) REVERT: A 227 GLU cc_start: 0.9474 (tm-30) cc_final: 0.9168 (tm-30) REVERT: B 17 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7131 (p90) REVERT: B 48 GLU cc_start: 0.9075 (tp30) cc_final: 0.8783 (tm-30) REVERT: B 81 GLN cc_start: 0.9502 (tt0) cc_final: 0.9221 (tp-100) REVERT: B 101 ARG cc_start: 0.9522 (ttm170) cc_final: 0.9065 (ttp-110) REVERT: B 205 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 227 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9035 (tm-30) REVERT: C 17 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7347 (p90) REVERT: C 42 GLU cc_start: 0.8173 (pp20) cc_final: 0.7735 (pp20) REVERT: C 100 MET cc_start: 0.9338 (ttp) cc_final: 0.9111 (ppp) REVERT: C 101 ARG cc_start: 0.9409 (ttm170) cc_final: 0.9024 (ttp-110) REVERT: C 227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9211 (tm-30) REVERT: D 17 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6959 (p90) REVERT: D 48 GLU cc_start: 0.9116 (tp30) cc_final: 0.8545 (tm-30) REVERT: D 101 ARG cc_start: 0.9601 (ttm170) cc_final: 0.9158 (ttp-110) REVERT: D 213 MET cc_start: 0.9189 (mmm) cc_final: 0.8942 (mmp) REVERT: D 224 ASN cc_start: 0.8811 (m-40) cc_final: 0.8417 (m110) REVERT: D 227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9155 (tm-30) REVERT: E 17 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7132 (p90) REVERT: E 81 GLN cc_start: 0.9511 (tt0) cc_final: 0.9231 (tp-100) REVERT: E 101 ARG cc_start: 0.9525 (ttm170) cc_final: 0.9063 (ttp-110) REVERT: E 205 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8715 (mm-30) REVERT: E 227 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9039 (tm-30) REVERT: F 17 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7344 (p90) REVERT: F 100 MET cc_start: 0.9339 (ttp) cc_final: 0.9116 (ppp) REVERT: F 101 ARG cc_start: 0.9407 (ttm170) cc_final: 0.9035 (ttp-110) REVERT: F 227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9212 (tm-30) outliers start: 33 outliers final: 22 residues processed: 204 average time/residue: 0.1848 time to fit residues: 55.2833 Evaluate side-chains 206 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10218 Z= 0.226 Angle : 0.701 11.379 13824 Z= 0.361 Chirality : 0.038 0.145 1572 Planarity : 0.004 0.038 1662 Dihedral : 5.572 48.652 1326 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 28.42 % Favored : 68.76 % 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: 1.22 (0.25), residues: 1200 helix: 1.64 (0.19), residues: 828 sheet: 1.80 (0.65), residues: 66 loop : -1.78 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 25 HIS 0.002 0.001 HIS D 74 PHE 0.031 0.001 PHE E 30 TYR 0.018 0.001 TYR D 92 ARG 0.001 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7286 (p90) REVERT: A 48 GLU cc_start: 0.9136 (tp30) cc_final: 0.8662 (tm-30) REVERT: A 100 MET cc_start: 0.9401 (ttp) cc_final: 0.9174 (ppp) REVERT: A 101 ARG cc_start: 0.9445 (ttm170) cc_final: 0.9067 (ttp-110) REVERT: A 213 MET cc_start: 0.9196 (mmm) cc_final: 0.8922 (mmp) REVERT: A 227 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9193 (tm-30) REVERT: B 17 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7264 (p90) REVERT: B 48 GLU cc_start: 0.9099 (tp30) cc_final: 0.8787 (tm-30) REVERT: B 81 GLN cc_start: 0.9523 (tt0) cc_final: 0.9220 (tp-100) REVERT: B 101 ARG cc_start: 0.9531 (ttm170) cc_final: 0.9086 (ttp-110) REVERT: B 213 MET cc_start: 0.9202 (mmm) cc_final: 0.8910 (mmp) REVERT: B 227 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9074 (tm-30) REVERT: C 17 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7338 (p90) REVERT: C 100 MET cc_start: 0.9330 (ttp) cc_final: 0.9117 (ppp) REVERT: C 101 ARG cc_start: 0.9414 (ttm170) cc_final: 0.9033 (ttp-110) REVERT: D 17 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7210 (p90) REVERT: D 101 ARG cc_start: 0.9605 (ttm170) cc_final: 0.9170 (ttp-110) REVERT: D 213 MET cc_start: 0.9207 (mmm) cc_final: 0.8962 (mmp) REVERT: D 224 ASN cc_start: 0.8822 (m-40) cc_final: 0.8419 (m110) REVERT: D 227 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9170 (tm-30) REVERT: E 17 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7268 (p90) REVERT: E 81 GLN cc_start: 0.9523 (tt0) cc_final: 0.9222 (tp-100) REVERT: E 101 ARG cc_start: 0.9533 (ttm170) cc_final: 0.9084 (ttp-110) REVERT: E 213 MET cc_start: 0.9204 (mmm) cc_final: 0.8913 (mmp) REVERT: E 227 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9069 (tm-30) REVERT: F 17 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7341 (p90) REVERT: F 100 MET cc_start: 0.9329 (ttp) cc_final: 0.9114 (ppp) REVERT: F 101 ARG cc_start: 0.9406 (ttm170) cc_final: 0.9026 (ttp-110) outliers start: 31 outliers final: 19 residues processed: 192 average time/residue: 0.1886 time to fit residues: 52.6755 Evaluate side-chains 196 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0070 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10218 Z= 0.195 Angle : 0.732 11.694 13824 Z= 0.371 Chirality : 0.038 0.145 1572 Planarity : 0.004 0.036 1662 Dihedral : 5.549 49.505 1326 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.82 % Allowed : 28.60 % Favored : 68.58 % 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: 1.23 (0.25), residues: 1200 helix: 1.62 (0.19), residues: 828 sheet: 1.84 (0.66), residues: 66 loop : -1.73 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 25 HIS 0.002 0.000 HIS D 74 PHE 0.033 0.001 PHE E 30 TYR 0.017 0.001 TYR D 92 ARG 0.001 0.000 ARG B 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7252 (p90) REVERT: A 42 GLU cc_start: 0.8321 (pp20) cc_final: 0.8068 (mt-10) REVERT: A 48 GLU cc_start: 0.9093 (tp30) cc_final: 0.8700 (tm-30) REVERT: A 100 MET cc_start: 0.9396 (ttp) cc_final: 0.9185 (ppp) REVERT: A 101 ARG cc_start: 0.9444 (ttm170) cc_final: 0.9088 (ptm-80) REVERT: A 213 MET cc_start: 0.9177 (mmm) cc_final: 0.8907 (mmp) REVERT: A 227 GLU cc_start: 0.9479 (tm-30) cc_final: 0.9187 (tm-30) REVERT: B 17 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7265 (p90) REVERT: B 48 GLU cc_start: 0.9057 (tp30) cc_final: 0.8781 (tm-30) REVERT: B 81 GLN cc_start: 0.9514 (tt0) cc_final: 0.9216 (tp-100) REVERT: B 101 ARG cc_start: 0.9525 (ttm170) cc_final: 0.9076 (ttp-110) REVERT: B 213 MET cc_start: 0.9194 (mmm) cc_final: 0.8906 (mmp) REVERT: B 227 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9063 (tm-30) REVERT: C 17 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7301 (p90) REVERT: C 100 MET cc_start: 0.9337 (ttp) cc_final: 0.9121 (ppp) REVERT: C 101 ARG cc_start: 0.9415 (ttm170) cc_final: 0.9038 (ttp-110) REVERT: D 17 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7076 (p90) REVERT: D 101 ARG cc_start: 0.9601 (ttm170) cc_final: 0.9163 (ttp-110) REVERT: D 213 MET cc_start: 0.9194 (mmm) cc_final: 0.8944 (mmp) REVERT: D 224 ASN cc_start: 0.8811 (m-40) cc_final: 0.8412 (m110) REVERT: D 227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9146 (tm-30) REVERT: E 17 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7178 (p90) REVERT: E 81 GLN cc_start: 0.9511 (tt0) cc_final: 0.9228 (tp-100) REVERT: E 101 ARG cc_start: 0.9529 (ttm170) cc_final: 0.9074 (ttp-110) REVERT: E 213 MET cc_start: 0.9198 (mmm) cc_final: 0.8911 (mmp) REVERT: E 227 GLU cc_start: 0.9447 (tm-30) cc_final: 0.9060 (tm-30) REVERT: F 17 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7315 (p90) REVERT: F 100 MET cc_start: 0.9330 (ttp) cc_final: 0.9114 (ppp) REVERT: F 101 ARG cc_start: 0.9405 (ttm170) cc_final: 0.9030 (ttp-110) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.1863 time to fit residues: 51.1577 Evaluate side-chains 203 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.072844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057115 restraints weight = 42724.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058892 restraints weight = 21934.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060070 restraints weight = 14265.578| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10218 Z= 0.203 Angle : 0.718 11.352 13824 Z= 0.368 Chirality : 0.038 0.145 1572 Planarity : 0.004 0.037 1662 Dihedral : 5.502 47.729 1326 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.91 % Allowed : 28.69 % Favored : 68.40 % 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: 1.25 (0.25), residues: 1200 helix: 1.62 (0.19), residues: 828 sheet: 2.04 (0.67), residues: 66 loop : -1.72 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 25 HIS 0.002 0.000 HIS D 74 PHE 0.032 0.001 PHE E 30 TYR 0.018 0.001 TYR D 92 ARG 0.001 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.95 seconds wall clock time: 35 minutes 45.10 seconds (2145.10 seconds total)