Starting phenix.real_space_refine on Sat Dec 9 06:23:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/12_2023/5fn3_3238.pdb" } resolution = 4.1 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= 0.006 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 39 5.16 5 C 6738 2.51 5 N 1679 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10291 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2234 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Time building chain proxies: 5.82, per 1000 atoms: 0.57 Number of scatterers: 10291 At special positions: 0 Unit cell: (92.4, 144.2, 110.6, 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 39 16.00 O 1835 8.00 N 1679 7.00 C 6738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.01 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2482 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 60.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.230A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.691A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.181A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.514A pdb=" N ASN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.586A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.747A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.677A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.941A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.627A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 126 through 156 removed outlier: 3.909A pdb=" N THR B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 190 removed outlier: 3.779A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.611A pdb=" N VAL B 393 " --> pdb=" O TYR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.515A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.235A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 106 removed outlier: 3.676A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 141 removed outlier: 5.093A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.624A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.903A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.713A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.598A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.843A pdb=" N VAL D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'G' and resid 5 through 13 Processing helix chain 'G' and resid 16 through 24 Processing sheet with id= AA, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.490A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 69 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id= AC, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.745A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 365 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 602 through 605 Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.842A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1839 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: 3.11 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1684 1.32 - 1.45: 3051 1.45 - 1.58: 5751 1.58 - 1.71: 10 1.71 - 1.84: 59 Bond restraints: 10555 Sorted by residual: bond pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 1.523 1.603 -0.080 1.34e-02 5.57e+03 3.53e+01 bond pdb=" CA LEU B 262 " pdb=" C LEU B 262 " ideal model delta sigma weight residual 1.523 1.591 -0.067 1.34e-02 5.57e+03 2.53e+01 bond pdb=" C ILE C 127 " pdb=" O ILE C 127 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.13e-02 7.83e+03 2.20e+01 bond pdb=" CA HIS B 214 " pdb=" C HIS B 214 " ideal model delta sigma weight residual 1.522 1.564 -0.042 9.30e-03 1.16e+04 2.07e+01 bond pdb=" N LYS B 429 " pdb=" CA LYS B 429 " ideal model delta sigma weight residual 1.457 1.516 -0.058 1.29e-02 6.01e+03 2.04e+01 ... (remaining 10550 not shown) Histogram of bond angle deviations from ideal: 97.85 - 106.46: 333 106.46 - 115.07: 6567 115.07 - 123.67: 6322 123.67 - 132.28: 1146 132.28 - 140.89: 31 Bond angle restraints: 14399 Sorted by residual: angle pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 120.38 130.82 -10.44 1.03e+00 9.43e-01 1.03e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 121.52 -10.82 1.22e+00 6.72e-01 7.87e+01 angle pdb=" C THR B 256 " pdb=" CA THR B 256 " pdb=" CB THR B 256 " ideal model delta sigma weight residual 110.88 97.85 13.03 1.57e+00 4.06e-01 6.89e+01 angle pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.83 115.96 4.87 6.10e-01 2.69e+00 6.38e+01 angle pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" CD PRO B 117 " ideal model delta sigma weight residual 112.00 101.66 10.34 1.40e+00 5.10e-01 5.45e+01 ... (remaining 14394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 5493 23.44 - 46.88: 557 46.88 - 70.32: 93 70.32 - 93.77: 17 93.77 - 117.21: 1 Dihedral angle restraints: 6161 sinusoidal: 2316 harmonic: 3845 Sorted by residual: dihedral pdb=" CA GLY B 111 " pdb=" C GLY B 111 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " ideal model delta harmonic sigma weight residual -180.00 -62.79 -117.21 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CA PRO B 117 " pdb=" C PRO B 117 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta harmonic sigma weight residual 180.00 87.92 92.08 0 5.00e+00 4.00e-02 3.39e+02 dihedral pdb=" CA ALA G 17 " pdb=" C ALA G 17 " pdb=" N ALA G 18 " pdb=" CA ALA G 18 " ideal model delta harmonic sigma weight residual 180.00 94.37 85.63 0 5.00e+00 4.00e-02 2.93e+02 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1373 0.120 - 0.241: 250 0.241 - 0.361: 42 0.361 - 0.482: 8 0.482 - 0.602: 5 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" C PRO B 117 " pdb=" CB PRO B 117 " both_signs ideal model delta sigma weight residual False 2.72 2.12 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA THR B 122 " pdb=" N THR B 122 " pdb=" C THR B 122 " pdb=" CB THR B 122 " both_signs ideal model delta sigma weight residual False 2.53 1.94 0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA PHE A 525 " pdb=" N PHE A 525 " pdb=" C PHE A 525 " pdb=" CB PHE A 525 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 1675 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " 0.082 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO A 560 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 155 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS B 155 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B 155 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR B 156 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A 211 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.048 5.00e-02 4.00e+02 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 6 1.80 - 2.57: 96 2.57 - 3.35: 13963 3.35 - 4.12: 25650 4.12 - 4.90: 45649 Nonbonded interactions: 85364 Sorted by model distance: nonbonded pdb=" O ALA G 15 " pdb=" CB ALA G 18 " model vdw 1.021 3.460 nonbonded pdb=" SD MET B 146 " pdb=" O ALA G 23 " model vdw 1.099 3.400 nonbonded pdb=" OH TYR B 115 " pdb=" CA ALA G 19 " model vdw 1.163 3.470 nonbonded pdb=" OH TYR B 115 " pdb=" N ALA G 19 " model vdw 1.283 2.520 nonbonded pdb=" O ALA G 12 " pdb=" CB ALA G 14 " model vdw 1.451 3.460 ... (remaining 85359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.000 Extract box with map and model: 1.880 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.380 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 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 : 0.011 0.100 10555 Z= 0.729 Angle : 1.812 15.892 14399 Z= 1.274 Chirality : 0.102 0.602 1678 Planarity : 0.009 0.126 1792 Dihedral : 18.644 117.206 3664 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 3.99 % Allowed : 10.74 % Favored : 85.28 % Rotamer: Outliers : 11.34 % Allowed : 17.24 % Favored : 71.42 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.40 % Twisted Proline : 3.51 % Twisted General : 2.07 % 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: -1.54 (0.21), residues: 1304 helix: 1.17 (0.16), residues: 733 sheet: -3.06 (0.39), residues: 108 loop : -4.37 (0.22), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 58 HIS 0.010 0.003 HIS B 214 PHE 0.045 0.005 PHE B 411 TYR 0.050 0.004 TYR C 69 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 264 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 30 residues processed: 341 average time/residue: 0.2007 time to fit residues: 98.9778 Evaluate side-chains 190 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1049 time to fit residues: 7.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 573 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN C 68 GLN C 136 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10555 Z= 0.289 Angle : 0.906 13.070 14399 Z= 0.466 Chirality : 0.048 0.317 1678 Planarity : 0.008 0.151 1792 Dihedral : 8.131 63.460 1416 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 1.38 % Allowed : 8.97 % Favored : 89.65 % Rotamer: Outliers : 0.45 % Allowed : 5.63 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.48 % Twisted Proline : 1.75 % Twisted General : 1.12 % 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: -0.58 (0.24), residues: 1304 helix: 1.79 (0.19), residues: 764 sheet: -2.54 (0.41), residues: 124 loop : -4.09 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 247 HIS 0.012 0.001 HIS C 197 PHE 0.036 0.003 PHE A 302 TYR 0.041 0.003 TYR B 115 ARG 0.004 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 216 average time/residue: 0.1875 time to fit residues: 60.9414 Evaluate side-chains 140 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 194 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10555 Z= 0.297 Angle : 0.815 11.505 14399 Z= 0.425 Chirality : 0.045 0.261 1678 Planarity : 0.007 0.123 1792 Dihedral : 7.301 52.478 1416 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.20 % Favored : 89.72 % Rotamer: Outliers : 0.36 % Allowed : 3.27 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.64 % 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: -0.68 (0.24), residues: 1304 helix: 1.51 (0.19), residues: 760 sheet: -2.32 (0.42), residues: 120 loop : -3.71 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 247 HIS 0.014 0.002 HIS C 197 PHE 0.032 0.003 PHE A 302 TYR 0.028 0.002 TYR B 115 ARG 0.004 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 189 average time/residue: 0.1950 time to fit residues: 55.4199 Evaluate side-chains 131 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.172 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0961 time to fit residues: 1.6902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10555 Z= 0.226 Angle : 0.774 12.776 14399 Z= 0.397 Chirality : 0.044 0.310 1678 Planarity : 0.007 0.144 1792 Dihedral : 6.980 50.939 1416 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.36 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.56 % 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: -0.53 (0.24), residues: 1304 helix: 1.51 (0.19), residues: 758 sheet: -2.10 (0.44), residues: 114 loop : -3.43 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 247 HIS 0.009 0.001 HIS C 197 PHE 0.032 0.002 PHE A 327 TYR 0.027 0.002 TYR B 106 ARG 0.005 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1897 time to fit residues: 50.2475 Evaluate side-chains 128 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10555 Z= 0.204 Angle : 0.739 11.389 14399 Z= 0.380 Chirality : 0.042 0.256 1678 Planarity : 0.006 0.118 1792 Dihedral : 6.544 48.753 1416 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.21 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.48 % 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: -0.46 (0.24), residues: 1304 helix: 1.47 (0.19), residues: 757 sheet: -1.84 (0.45), residues: 119 loop : -3.24 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 247 HIS 0.009 0.001 HIS C 197 PHE 0.024 0.002 PHE B 465 TYR 0.024 0.002 TYR B 106 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1960 time to fit residues: 52.9736 Evaluate side-chains 135 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 0.0270 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 478 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10555 Z= 0.208 Angle : 0.723 12.779 14399 Z= 0.370 Chirality : 0.042 0.282 1678 Planarity : 0.006 0.120 1792 Dihedral : 6.349 47.132 1416 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.82 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.40 % 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 (0.24), residues: 1304 helix: 1.43 (0.18), residues: 755 sheet: -1.62 (0.46), residues: 119 loop : -3.18 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 247 HIS 0.010 0.001 HIS C 197 PHE 0.027 0.002 PHE B 465 TYR 0.020 0.002 TYR D 56 ARG 0.009 0.001 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1917 time to fit residues: 51.3008 Evaluate side-chains 129 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 428 GLN A 444 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10555 Z= 0.250 Angle : 0.753 11.661 14399 Z= 0.383 Chirality : 0.042 0.261 1678 Planarity : 0.006 0.103 1792 Dihedral : 6.202 47.279 1416 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.28 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1304 helix: 1.52 (0.18), residues: 743 sheet: -1.64 (0.45), residues: 119 loop : -2.96 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 247 HIS 0.009 0.002 HIS C 197 PHE 0.032 0.002 PHE A 210 TYR 0.032 0.002 TYR D 18 ARG 0.007 0.001 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2178 time to fit residues: 57.5436 Evaluate side-chains 127 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 428 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10555 Z= 0.234 Angle : 0.742 12.353 14399 Z= 0.379 Chirality : 0.043 0.261 1678 Planarity : 0.006 0.096 1792 Dihedral : 6.154 45.901 1416 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.67 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.40 % 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 (0.24), residues: 1304 helix: 1.39 (0.19), residues: 746 sheet: -1.71 (0.45), residues: 115 loop : -2.87 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 247 HIS 0.015 0.002 HIS C 197 PHE 0.027 0.002 PHE B 465 TYR 0.026 0.002 TYR B 466 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1956 time to fit residues: 51.5352 Evaluate side-chains 126 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10555 Z= 0.207 Angle : 0.742 11.602 14399 Z= 0.377 Chirality : 0.042 0.216 1678 Planarity : 0.005 0.065 1792 Dihedral : 6.123 45.656 1416 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.21 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.32 % 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 (0.24), residues: 1304 helix: 1.35 (0.19), residues: 744 sheet: -1.71 (0.44), residues: 117 loop : -2.83 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 247 HIS 0.010 0.002 HIS C 171 PHE 0.031 0.002 PHE B 465 TYR 0.018 0.002 TYR C 90 ARG 0.006 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1896 time to fit residues: 49.9612 Evaluate side-chains 124 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 454 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10555 Z= 0.203 Angle : 0.744 12.089 14399 Z= 0.376 Chirality : 0.042 0.214 1678 Planarity : 0.005 0.064 1792 Dihedral : 5.918 43.475 1416 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.44 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.32 % 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 (0.24), residues: 1304 helix: 1.30 (0.19), residues: 745 sheet: -1.62 (0.45), residues: 117 loop : -2.78 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 247 HIS 0.009 0.001 HIS C 197 PHE 0.025 0.002 PHE B 465 TYR 0.018 0.002 TYR D 56 ARG 0.007 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1893 time to fit residues: 48.8854 Evaluate side-chains 129 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 103 optimal weight: 9.9990 chunk 43 optimal weight: 0.0770 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 2.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.050171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043179 restraints weight = 75846.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044334 restraints weight = 48163.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045064 restraints weight = 33241.578| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10555 Z= 0.220 Angle : 0.745 11.678 14399 Z= 0.377 Chirality : 0.042 0.211 1678 Planarity : 0.005 0.064 1792 Dihedral : 5.840 43.999 1416 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.51 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.16 % 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: -0.49 (0.24), residues: 1304 helix: 1.24 (0.18), residues: 744 sheet: -1.65 (0.45), residues: 119 loop : -2.76 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 247 HIS 0.009 0.001 HIS C 197 PHE 0.054 0.002 PHE A 682 TYR 0.020 0.002 TYR D 18 ARG 0.003 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.26 seconds wall clock time: 38 minutes 21.15 seconds (2301.15 seconds total)