Starting phenix.real_space_refine on Thu Nov 14 06:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jps_36488/11_2024/8jps_36488.cif" } resolution = 3.65 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= 0.006 sd= 0.041 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 34 5.16 5 C 3034 2.51 5 N 751 2.21 5 O 797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4616 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1890 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 427 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1884 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 415 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 3.62, per 1000 atoms: 0.78 Number of scatterers: 4616 At special positions: 0 Unit cell: (132.383, 83.5612, 61.0279, 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 34 16.00 O 797 8.00 N 751 7.00 C 3034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 36 " distance=2.03 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS C 12 " - pdb=" SG CYS C 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 568.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 67.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 82 removed outlier: 4.345A pdb=" N THR B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.824A pdb=" N PHE B 88 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 89' Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.624A pdb=" N LEU B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 125 through 158 removed outlier: 6.542A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 226 removed outlier: 4.483A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 268 Proline residue: B 255 - end of helix removed outlier: 3.894A pdb=" N LEU B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 295 Processing helix chain 'B' and resid 295 through 311 Proline residue: B 301 - end of helix Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 82 removed outlier: 4.613A pdb=" N THR A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.692A pdb=" N PHE A 88 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.667A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 125 through 153 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 203 through 227 removed outlier: 4.398A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.742A pdb=" N LEU A 260 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 295 through 312 Proline residue: A 301 - end of helix removed outlier: 3.580A pdb=" N THR A 312 " --> pdb=" O CYS A 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.559A pdb=" N GLN C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.565A pdb=" N GLY B 189 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 25 through 29 removed outlier: 6.681A pdb=" N LYS D 44 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR D 28 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE D 42 " --> pdb=" O TYR D 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 191 removed outlier: 4.021A pdb=" N LEU A 194 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.812A pdb=" N VAL C 41 " --> pdb=" O ALA C 53 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.34 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: 1418 1.34 - 1.46: 1082 1.46 - 1.58: 2194 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 4732 Sorted by residual: bond pdb=" N LYS D 18 " pdb=" CA LYS D 18 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.34e-02 5.57e+03 3.60e+00 bond pdb=" N TRP A 242 " pdb=" CA TRP A 242 " ideal model delta sigma weight residual 1.454 1.476 -0.022 1.17e-02 7.31e+03 3.50e+00 bond pdb=" N GLU B 46 " pdb=" CA GLU B 46 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.88e+00 bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.90e-02 2.77e+03 1.75e+00 bond pdb=" C LEU A 221 " pdb=" N PRO A 222 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.30e-02 5.92e+03 1.17e+00 ... (remaining 4727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 6160 1.33 - 2.67: 259 2.67 - 4.00: 48 4.00 - 5.33: 24 5.33 - 6.67: 7 Bond angle restraints: 6498 Sorted by residual: angle pdb=" N TRP A 242 " pdb=" CA TRP A 242 " pdb=" CB TRP A 242 " ideal model delta sigma weight residual 110.39 115.64 -5.25 1.59e+00 3.96e-01 1.09e+01 angle pdb=" C GLU B 46 " pdb=" N ALA B 47 " pdb=" CA ALA B 47 " ideal model delta sigma weight residual 120.88 115.74 5.14 1.62e+00 3.81e-01 1.01e+01 angle pdb=" CA LYS D 18 " pdb=" C LYS D 18 " pdb=" O LYS D 18 " ideal model delta sigma weight residual 121.87 118.23 3.64 1.16e+00 7.43e-01 9.87e+00 angle pdb=" O TRP A 242 " pdb=" C TRP A 242 " pdb=" N MET A 243 " ideal model delta sigma weight residual 121.83 125.84 -4.01 1.28e+00 6.10e-01 9.81e+00 angle pdb=" C ALA B 61 " pdb=" N LEU B 62 " pdb=" CA LEU B 62 " ideal model delta sigma weight residual 120.09 123.81 -3.72 1.25e+00 6.40e-01 8.87e+00 ... (remaining 6493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 2523 16.73 - 33.46: 166 33.46 - 50.19: 43 50.19 - 66.92: 7 66.92 - 83.65: 3 Dihedral angle restraints: 2742 sinusoidal: 910 harmonic: 1832 Sorted by residual: dihedral pdb=" CB CYS B 129 " pdb=" SG CYS B 129 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual 93.00 160.77 -67.77 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 276 " pdb=" CB CYS A 276 " ideal model delta sinusoidal sigma weight residual -86.00 -150.90 64.90 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA ASP B 58 " pdb=" C ASP B 58 " pdb=" N ASP B 59 " pdb=" CA ASP B 59 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 2739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 504 0.029 - 0.058: 193 0.058 - 0.087: 59 0.087 - 0.116: 49 0.116 - 0.145: 8 Chirality restraints: 813 Sorted by residual: chirality pdb=" CA THR B 300 " pdb=" N THR B 300 " pdb=" C THR B 300 " pdb=" CB THR B 300 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA GLU A 46 " pdb=" N GLU A 46 " pdb=" C GLU A 46 " pdb=" CB GLU A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA THR A 300 " pdb=" N THR A 300 " pdb=" C THR A 300 " pdb=" CB THR A 300 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 810 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 136 " -0.023 2.00e-02 2.50e+03 1.65e-02 6.85e+00 pdb=" CG TRP A 136 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 136 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 136 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 136 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 136 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 136 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 136 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 136 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 216 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ALA A 216 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 216 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 216 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ALA B 216 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA B 216 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE B 217 " 0.013 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1431 2.83 - 3.35: 4786 3.35 - 3.86: 7403 3.86 - 4.38: 7931 4.38 - 4.90: 13694 Nonbonded interactions: 35245 Sorted by model distance: nonbonded pdb=" O SER A 53 " pdb=" ND2 ASN A 55 " model vdw 2.310 3.120 nonbonded pdb=" OE1 GLN A 143 " pdb=" NE1 TRP A 249 " model vdw 2.350 3.120 nonbonded pdb=" O SER B 122 " pdb=" OG1 THR B 123 " model vdw 2.356 3.040 nonbonded pdb=" O PHE B 264 " pdb=" OG SER B 268 " model vdw 2.361 3.040 nonbonded pdb=" O SER A 122 " pdb=" OG1 THR A 123 " model vdw 2.365 3.040 ... (remaining 35240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 46 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 through 242 or (resid 243 and (name N o \ r name CA or name C or name O or name CB )) or resid 244 through 312)) } ncs_group { reference = (chain 'C' and (resid 8 through 42 or (resid 43 through 44 and (name N or name C \ A or name C or name O or name CB )) or resid 45 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 61 or (resid 62 through 66 and (name N or name CA or name C or name O or name CB \ )) or resid 67 through 70)) selection = (chain 'D' and (resid 8 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 31 or (resi \ d 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throug \ h 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or re \ sid 51 through 55 or (resid 56 through 59 and (name N or name CA or name C or na \ me O or name CB )) or resid 60 through 62 or (resid 63 through 66 and (name N or \ name CA or name C or name O or name CB )) or resid 67 through 70)) } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.360 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4732 Z= 0.201 Angle : 0.691 6.666 6498 Z= 0.380 Chirality : 0.041 0.145 813 Planarity : 0.004 0.035 791 Dihedral : 12.409 83.654 1530 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.35), residues: 628 helix: 0.80 (0.29), residues: 364 sheet: 0.66 (1.16), residues: 24 loop : -1.96 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 136 HIS 0.004 0.001 HIS A 309 PHE 0.034 0.002 PHE B 109 TYR 0.007 0.002 TYR A 137 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.5704 (t0) cc_final: 0.5482 (t0) REVERT: B 288 LEU cc_start: 0.7434 (tp) cc_final: 0.7096 (tt) REVERT: A 136 TRP cc_start: 0.7612 (t-100) cc_final: 0.7014 (t60) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1419 time to fit residues: 21.0391 Evaluate side-chains 92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN D 23 GLN A 143 GLN A 150 HIS C 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4732 Z= 0.246 Angle : 0.671 7.137 6498 Z= 0.341 Chirality : 0.041 0.129 813 Planarity : 0.005 0.048 791 Dihedral : 4.893 20.361 654 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.37 % Allowed : 13.36 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.34), residues: 628 helix: 0.67 (0.29), residues: 366 sheet: 0.71 (1.13), residues: 24 loop : -2.00 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 136 HIS 0.004 0.001 HIS A 150 PHE 0.027 0.002 PHE B 81 TYR 0.012 0.002 TYR C 28 ARG 0.004 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.468 Fit side-chains REVERT: B 55 ASN cc_start: 0.6093 (t0) cc_final: 0.5750 (t0) REVERT: B 254 TRP cc_start: 0.5825 (t-100) cc_final: 0.5575 (t-100) REVERT: B 288 LEU cc_start: 0.7421 (tp) cc_final: 0.7117 (tt) REVERT: A 112 VAL cc_start: 0.8079 (p) cc_final: 0.7778 (t) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 0.1167 time to fit residues: 15.2666 Evaluate side-chains 96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 0.0670 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN D 23 GLN A 279 GLN C 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4732 Z= 0.199 Angle : 0.652 8.259 6498 Z= 0.329 Chirality : 0.041 0.295 813 Planarity : 0.005 0.045 791 Dihedral : 4.752 19.062 654 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.72 % Allowed : 18.10 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.34), residues: 628 helix: 0.59 (0.28), residues: 376 sheet: 0.32 (1.07), residues: 24 loop : -2.01 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 136 HIS 0.002 0.001 HIS A 256 PHE 0.022 0.002 PHE B 81 TYR 0.008 0.001 TYR D 13 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.526 Fit side-chains REVERT: B 112 VAL cc_start: 0.8135 (p) cc_final: 0.7773 (t) REVERT: B 288 LEU cc_start: 0.7452 (tp) cc_final: 0.7159 (tt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.1215 time to fit residues: 16.2296 Evaluate side-chains 97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4732 Z= 0.187 Angle : 0.624 8.817 6498 Z= 0.313 Chirality : 0.040 0.153 813 Planarity : 0.005 0.045 791 Dihedral : 4.563 18.403 654 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.80 % Allowed : 19.83 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 628 helix: 0.78 (0.28), residues: 370 sheet: -0.12 (1.05), residues: 24 loop : -1.96 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 136 HIS 0.006 0.001 HIS B 296 PHE 0.023 0.002 PHE A 264 TYR 0.014 0.001 TYR C 28 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.516 Fit side-chains REVERT: B 146 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 288 LEU cc_start: 0.7469 (tp) cc_final: 0.7263 (tp) REVERT: D 23 GLN cc_start: 0.8438 (tp40) cc_final: 0.8204 (tp-100) outliers start: 13 outliers final: 6 residues processed: 101 average time/residue: 0.1100 time to fit residues: 15.7661 Evaluate side-chains 101 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4732 Z= 0.219 Angle : 0.677 11.865 6498 Z= 0.332 Chirality : 0.041 0.150 813 Planarity : 0.005 0.044 791 Dihedral : 4.592 18.049 654 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.23 % Allowed : 19.40 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.34), residues: 628 helix: 0.71 (0.28), residues: 370 sheet: -0.42 (1.06), residues: 24 loop : -1.91 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 136 HIS 0.004 0.001 HIS B 296 PHE 0.019 0.002 PHE B 81 TYR 0.007 0.001 TYR D 28 ARG 0.001 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.478 Fit side-chains REVERT: B 146 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 147 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6423 (mm) REVERT: D 23 GLN cc_start: 0.8491 (tp40) cc_final: 0.8291 (tp-100) REVERT: A 221 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6613 (tt) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.1166 time to fit residues: 15.8396 Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4732 Z= 0.384 Angle : 0.796 10.691 6498 Z= 0.391 Chirality : 0.045 0.149 813 Planarity : 0.005 0.045 791 Dihedral : 5.047 18.792 654 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.66 % Allowed : 20.47 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.34), residues: 628 helix: 0.32 (0.28), residues: 370 sheet: -1.42 (0.91), residues: 34 loop : -2.04 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 136 HIS 0.004 0.001 HIS A 210 PHE 0.028 0.003 PHE B 81 TYR 0.010 0.002 TYR A 137 ARG 0.005 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.523 Fit side-chains REVERT: B 147 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6514 (mm) REVERT: A 147 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6713 (mm) REVERT: A 221 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6815 (tt) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 0.1200 time to fit residues: 16.6956 Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.0000 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.0070 chunk 11 optimal weight: 5.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4732 Z= 0.201 Angle : 0.682 7.662 6498 Z= 0.339 Chirality : 0.041 0.227 813 Planarity : 0.005 0.043 791 Dihedral : 4.687 17.804 654 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.66 % Allowed : 23.06 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.34), residues: 628 helix: 0.66 (0.28), residues: 372 sheet: -1.34 (0.91), residues: 34 loop : -1.88 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.017 0.001 PHE A 264 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.533 Fit side-chains REVERT: B 147 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6262 (mm) REVERT: D 38 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5805 (ptt-90) REVERT: A 147 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6557 (mm) REVERT: A 221 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6621 (tt) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 0.1269 time to fit residues: 17.9527 Evaluate side-chains 106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 52 optimal weight: 0.0010 chunk 55 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4732 Z= 0.200 Angle : 0.691 10.775 6498 Z= 0.337 Chirality : 0.042 0.260 813 Planarity : 0.005 0.044 791 Dihedral : 4.592 17.306 654 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.88 % Allowed : 22.63 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.35), residues: 628 helix: 0.79 (0.28), residues: 370 sheet: -1.36 (0.92), residues: 34 loop : -1.80 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 136 HIS 0.002 0.001 HIS A 296 PHE 0.030 0.001 PHE A 264 TYR 0.012 0.001 TYR C 28 ARG 0.002 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.477 Fit side-chains REVERT: B 147 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6248 (mm) REVERT: D 38 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.5763 (ptt-90) REVERT: A 221 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6515 (tt) outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.1231 time to fit residues: 17.3828 Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4732 Z= 0.254 Angle : 0.740 11.460 6498 Z= 0.363 Chirality : 0.043 0.197 813 Planarity : 0.005 0.044 791 Dihedral : 4.646 17.144 654 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.45 % Allowed : 23.92 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.34), residues: 628 helix: 0.79 (0.28), residues: 366 sheet: -1.40 (0.93), residues: 34 loop : -1.82 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 254 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.002 PHE A 264 TYR 0.006 0.001 TYR A 199 ARG 0.001 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.525 Fit side-chains REVERT: B 147 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6428 (mm) REVERT: A 147 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6620 (mm) REVERT: A 221 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6619 (tt) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1254 time to fit residues: 17.5187 Evaluate side-chains 102 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4732 Z= 0.247 Angle : 0.746 11.264 6498 Z= 0.363 Chirality : 0.043 0.194 813 Planarity : 0.005 0.044 791 Dihedral : 4.645 17.320 654 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.02 % Allowed : 25.22 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.34), residues: 628 helix: 0.74 (0.28), residues: 366 sheet: -1.43 (0.92), residues: 34 loop : -1.80 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 254 HIS 0.003 0.001 HIS B 296 PHE 0.035 0.002 PHE A 264 TYR 0.020 0.002 TYR C 28 ARG 0.001 0.000 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.504 Fit side-chains REVERT: B 147 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6429 (mm) REVERT: A 147 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6655 (mm) REVERT: A 221 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6608 (tt) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.1231 time to fit residues: 16.3855 Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.123250 restraints weight = 10975.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.126177 restraints weight = 6121.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.128017 restraints weight = 4156.413| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4732 Z= 0.247 Angle : 0.751 11.131 6498 Z= 0.365 Chirality : 0.043 0.192 813 Planarity : 0.005 0.043 791 Dihedral : 4.630 17.380 654 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.45 % Allowed : 25.22 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.34), residues: 628 helix: 0.76 (0.28), residues: 366 sheet: -1.48 (0.92), residues: 34 loop : -1.81 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 254 HIS 0.003 0.001 HIS B 296 PHE 0.020 0.002 PHE A 264 TYR 0.007 0.001 TYR A 199 ARG 0.001 0.000 ARG D 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.70 seconds wall clock time: 23 minutes 36.06 seconds (1416.06 seconds total)