Starting phenix.real_space_refine on Mon Mar 11 11:30:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irm_35679/03_2024/8irm_35679.pdb" } resolution = 2.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5290 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'ADE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'ADE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.58 Number of scatterers: 8138 At special positions: 0 Unit cell: (93.61, 104.673, 100.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5290 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 68.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.389A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 180 through 202 removed outlier: 3.500A pdb=" N ILE A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.969A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.255A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.954A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.562A pdb=" N GLY A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.586A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 452 removed outlier: 4.039A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix removed outlier: 3.566A pdb=" N ILE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.694A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.581A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.703A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 removed outlier: 3.519A pdb=" N VAL B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 removed outlier: 4.142A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.145A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.884A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.735A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 removed outlier: 3.537A pdb=" N MET B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.232A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.559A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.769A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.810A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.810A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 241 through 242 517 hydrogen bonds defined for protein. 1467 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: 2.51 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 8 1.05 - 1.24: 1111 1.24 - 1.43: 2341 1.43 - 1.62: 4780 1.62 - 1.81: 84 Bond restraints: 8324 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.538 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.535 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C6 ADE A 701 " pdb=" N6 ADE A 701 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.527 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C6 ADE B 701 " pdb=" N6 ADE B 701 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 8319 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.61: 146 104.61 - 112.16: 4313 112.16 - 119.70: 2740 119.70 - 127.25: 4048 127.25 - 134.79: 87 Bond angle restraints: 11334 Sorted by residual: angle pdb=" C THR B 45 " pdb=" N PHE B 46 " pdb=" CA PHE B 46 " ideal model delta sigma weight residual 122.15 110.86 11.29 2.83e+00 1.25e-01 1.59e+01 angle pdb=" C THR A 45 " pdb=" N PHE A 46 " pdb=" CA PHE A 46 " ideal model delta sigma weight residual 122.15 111.15 11.00 2.83e+00 1.25e-01 1.51e+01 angle pdb=" C THR A 247 " pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N TYR B 524 " pdb=" CA TYR B 524 " pdb=" C TYR B 524 " ideal model delta sigma weight residual 112.58 108.84 3.74 1.22e+00 6.72e-01 9.42e+00 angle pdb=" C2 ADE A 701 " pdb=" N3 ADE A 701 " pdb=" C4 ADE A 701 " ideal model delta sigma weight residual 111.66 120.61 -8.95 3.00e+00 1.11e-01 8.90e+00 ... (remaining 11329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 4650 22.48 - 44.96: 213 44.96 - 67.44: 27 67.44 - 89.93: 3 89.93 - 112.41: 3 Dihedral angle restraints: 4896 sinusoidal: 1844 harmonic: 3052 Sorted by residual: dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 142.58 37.42 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 143.52 36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA PHE B 332 " pdb=" C PHE B 332 " pdb=" N ARG B 333 " pdb=" CA ARG B 333 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1081 0.051 - 0.102: 242 0.102 - 0.154: 27 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C6 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C5 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C6 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1353 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 248 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C LEU A 248 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 248 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL A 249 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 487 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 73 2.60 - 3.10: 6265 3.10 - 3.60: 10557 3.60 - 4.10: 14423 4.10 - 4.60: 23235 Nonbonded interactions: 54553 Sorted by model distance: nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.101 2.200 nonbonded pdb=" OD1 ASN A 163 " pdb=" OG SER A 437 " model vdw 2.119 2.200 nonbonded pdb=" OD1 ASN B 67 " pdb=" ND2 ASN B 163 " model vdw 2.126 2.350 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.157 2.200 nonbonded pdb=" OH TYR A 309 " pdb=" O VAL B 539 " model vdw 2.169 2.200 ... (remaining 54548 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.210 Extract box with map and model: 3.400 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.300 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.125 8316 Z= 0.453 Angle : 0.683 11.285 11320 Z= 0.335 Chirality : 0.042 0.256 1356 Planarity : 0.005 0.069 1398 Dihedral : 13.129 112.406 2932 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.86 (0.26), residues: 1076 helix: 1.25 (0.20), residues: 660 sheet: -4.69 (0.63), residues: 20 loop : -0.18 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 331 HIS 0.002 0.001 HIS A 364 PHE 0.035 0.002 PHE A 442 TYR 0.030 0.001 TYR A 418 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.863 Fit side-chains REVERT: A 32 ARG cc_start: 0.6316 (mpp-170) cc_final: 0.5980 (mtm-85) REVERT: B 32 ARG cc_start: 0.6378 (mpp-170) cc_final: 0.6040 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.2657 time to fit residues: 132.9547 Evaluate side-chains 83 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8316 Z= 0.135 Angle : 0.458 8.722 11320 Z= 0.240 Chirality : 0.037 0.133 1356 Planarity : 0.004 0.065 1398 Dihedral : 7.579 102.284 1230 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.28 % Allowed : 6.29 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.64 (0.27), residues: 1076 helix: 2.00 (0.20), residues: 664 sheet: -4.69 (0.63), residues: 20 loop : -0.13 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.002 0.001 HIS B 541 PHE 0.016 0.001 PHE A 442 TYR 0.008 0.001 TYR B 399 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.945 Fit side-chains REVERT: B 250 THR cc_start: 0.8489 (p) cc_final: 0.8241 (t) REVERT: B 548 GLU cc_start: 0.7340 (tp30) cc_final: 0.7106 (mt-10) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 1.2400 time to fit residues: 117.4348 Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8316 Z= 0.250 Angle : 0.489 9.646 11320 Z= 0.253 Chirality : 0.039 0.134 1356 Planarity : 0.004 0.062 1398 Dihedral : 7.159 98.579 1230 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 7.58 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.76 (0.27), residues: 1076 helix: 2.14 (0.20), residues: 664 sheet: -4.68 (0.63), residues: 20 loop : -0.16 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 PHE 0.027 0.002 PHE A 442 TYR 0.010 0.001 TYR B 399 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.941 Fit side-chains REVERT: A 494 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8325 (mtm) REVERT: B 250 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (t) REVERT: B 401 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7181 (mtp) outliers start: 16 outliers final: 7 residues processed: 87 average time/residue: 1.2681 time to fit residues: 117.5018 Evaluate side-chains 92 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8316 Z= 0.126 Angle : 0.423 9.074 11320 Z= 0.219 Chirality : 0.037 0.136 1356 Planarity : 0.004 0.065 1398 Dihedral : 6.661 96.035 1230 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 8.39 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.06 (0.27), residues: 1076 helix: 2.43 (0.20), residues: 666 sheet: -4.86 (0.60), residues: 20 loop : -0.16 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.001 0.000 HIS A 350 PHE 0.010 0.001 PHE A 166 TYR 0.008 0.001 TYR B 399 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 507 MET cc_start: 0.8745 (mmp) cc_final: 0.8429 (mmp) REVERT: B 401 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.6921 (mtp) REVERT: B 548 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6131 (mt-10) outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 1.2178 time to fit residues: 119.6366 Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 0.0050 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 8316 Z= 0.395 Angle : 0.563 10.894 11320 Z= 0.289 Chirality : 0.042 0.137 1356 Planarity : 0.004 0.060 1398 Dihedral : 6.665 92.083 1230 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.10 % Allowed : 8.51 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.61 (0.26), residues: 1076 helix: 2.03 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.53 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 380 HIS 0.004 0.001 HIS A 364 PHE 0.023 0.002 PHE A 442 TYR 0.013 0.001 TYR B 399 ARG 0.002 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7672 (ptt-90) cc_final: 0.7307 (ptt-90) REVERT: A 494 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: B 401 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7050 (mtp) REVERT: B 548 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6223 (mt-10) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 1.2796 time to fit residues: 119.8778 Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0470 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8316 Z= 0.123 Angle : 0.432 10.169 11320 Z= 0.221 Chirality : 0.037 0.122 1356 Planarity : 0.004 0.063 1398 Dihedral : 6.140 88.372 1230 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.93 % Allowed : 10.37 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 2.07 (0.27), residues: 1076 helix: 2.46 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.49 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.001 0.000 HIS B 541 PHE 0.010 0.001 PHE A 166 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7367 (ptt-90) REVERT: B 548 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6339 (mt-10) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 1.3467 time to fit residues: 123.0679 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8316 Z= 0.176 Angle : 0.444 10.622 11320 Z= 0.227 Chirality : 0.037 0.117 1356 Planarity : 0.004 0.063 1398 Dihedral : 5.854 82.530 1230 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.05 % Allowed : 10.37 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1076 helix: 2.53 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.44 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 541 PHE 0.011 0.001 PHE A 166 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7361 (ptt-90) REVERT: A 494 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: B 401 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.6938 (mpp) REVERT: B 548 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6342 (mt-10) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 1.3177 time to fit residues: 116.4241 Evaluate side-chains 85 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8316 Z= 0.133 Angle : 0.423 10.930 11320 Z= 0.215 Chirality : 0.037 0.116 1356 Planarity : 0.003 0.065 1398 Dihedral : 5.296 71.246 1230 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 10.72 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.35 (0.27), residues: 1076 helix: 2.68 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.37 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.001 0.000 HIS B 364 PHE 0.009 0.001 PHE A 166 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7676 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: A 494 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8185 (mtp) REVERT: B 401 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.6812 (mpp) REVERT: B 548 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6391 (mt-10) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 1.2661 time to fit residues: 113.0021 Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8316 Z= 0.227 Angle : 0.470 10.431 11320 Z= 0.241 Chirality : 0.038 0.118 1356 Planarity : 0.004 0.063 1398 Dihedral : 5.039 58.180 1230 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.52 % Allowed : 10.49 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 2.16 (0.26), residues: 1076 helix: 2.51 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.42 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 541 PHE 0.012 0.001 PHE A 442 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7643 (ptt-90) cc_final: 0.7354 (ptt-90) REVERT: A 494 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: B 401 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.6713 (mpp) REVERT: B 548 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6380 (mt-10) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 1.3431 time to fit residues: 122.7693 Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8316 Z= 0.316 Angle : 0.515 10.045 11320 Z= 0.265 Chirality : 0.040 0.119 1356 Planarity : 0.004 0.062 1398 Dihedral : 4.885 41.378 1230 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 10.49 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.85 (0.26), residues: 1076 helix: 2.26 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.52 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.002 PHE A 442 TYR 0.010 0.001 TYR B 399 ARG 0.001 0.000 ARG A 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7564 (ptt-90) cc_final: 0.7282 (ptt-90) REVERT: A 494 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: B 401 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.6651 (mpp) REVERT: B 548 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6324 (mt-10) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 1.3162 time to fit residues: 118.7866 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087648 restraints weight = 10299.239| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.89 r_work: 0.2900 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8316 Z= 0.143 Angle : 0.423 8.635 11320 Z= 0.219 Chirality : 0.037 0.116 1356 Planarity : 0.003 0.063 1398 Dihedral : 4.379 31.301 1230 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.40 % Allowed : 10.49 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.27), residues: 1076 helix: 2.57 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.41 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.001 0.001 HIS A 364 PHE 0.009 0.001 PHE A 166 TYR 0.007 0.001 TYR B 418 ARG 0.001 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.70 seconds wall clock time: 51 minutes 12.56 seconds (3072.56 seconds total)