Starting phenix.real_space_refine on Wed Mar 12 13:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.map" model { file = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2025/6sni_10258.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 P 1 5.49 5 S 31 5.16 5 C 4967 2.51 5 N 1156 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1725 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 163 Unusual residues: {'PTY': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.00, per 1000 atoms: 0.93 Number of scatterers: 7510 At special positions: 0 Unit cell: (115.92, 86.52, 113.4, 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 31 16.00 P 1 15.00 O 1355 8.00 N 1156 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.7% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 3.886A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 68 through 81 removed outlier: 3.749A pdb=" N ALA X 72 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN X 73 " --> pdb=" O ASP X 69 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 119 removed outlier: 3.674A pdb=" N ALA X 105 " --> pdb=" O PRO X 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.541A pdb=" N ILE X 147 " --> pdb=" O ARG X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 170 Processing helix chain 'X' and resid 172 through 185 removed outlier: 3.593A pdb=" N ALA X 179 " --> pdb=" O GLY X 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 Processing helix chain 'X' and resid 199 through 217 removed outlier: 4.425A pdb=" N MET X 203 " --> pdb=" O TYR X 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR X 207 " --> pdb=" O MET X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 231 removed outlier: 3.921A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 237 removed outlier: 6.959A pdb=" N MET X 235 " --> pdb=" O PHE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 253 removed outlier: 4.127A pdb=" N ALA X 245 " --> pdb=" O PRO X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 258 through 282 removed outlier: 3.904A pdb=" N LEU X 262 " --> pdb=" O ASN X 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 298 removed outlier: 3.596A pdb=" N ILE X 290 " --> pdb=" O GLY X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 removed outlier: 3.729A pdb=" N THR X 316 " --> pdb=" O PHE X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 325 Processing helix chain 'X' and resid 327 through 352 removed outlier: 3.647A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 358 through 374 removed outlier: 3.666A pdb=" N SER X 369 " --> pdb=" O ALA X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix Processing helix chain 'X' and resid 393 through 395 No H-bonds generated for 'chain 'X' and resid 393 through 395' Processing helix chain 'X' and resid 398 through 414 Processing helix chain 'X' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS X 421 " --> pdb=" O PRO X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 424 through 440 removed outlier: 3.508A pdb=" N ALA X 429 " --> pdb=" O HIS X 425 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN X 436 " --> pdb=" O PHE X 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY X 440 " --> pdb=" O ASN X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 476 through 491 removed outlier: 3.845A pdb=" N LYS X 480 " --> pdb=" O ASN X 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 481 " --> pdb=" O VAL X 477 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE X 482 " --> pdb=" O VAL X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 497 removed outlier: 3.623A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 536 removed outlier: 3.554A pdb=" N GLY X 518 " --> pdb=" O ASN X 514 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 527 " --> pdb=" O SER X 523 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE X 534 " --> pdb=" O TYR X 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.674A pdb=" N SER H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.624A pdb=" N SER H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR H 105 " --> pdb=" O TRP H 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 105' Processing helix chain 'H' and resid 194 through 198 removed outlier: 4.024A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.299A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.584A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.985A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.912A pdb=" N TYR H 111 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.186A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.386A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.800A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.898A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152 341 hydrogen bonds defined for protein. 947 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: 2.21 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1122 1.30 - 1.44: 2314 1.44 - 1.58: 4221 1.58 - 1.72: 33 1.72 - 1.86: 47 Bond restraints: 7737 Sorted by residual: bond pdb=" CAK Y01 H2202 " pdb=" CBD Y01 H2202 " ideal model delta sigma weight residual 1.525 1.160 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CAU Y01 H2202 " pdb=" CBI Y01 H2202 " ideal model delta sigma weight residual 1.530 1.166 0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAK Y01 X1606 " pdb=" CBD Y01 X1606 " ideal model delta sigma weight residual 1.525 1.162 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAU Y01 X1606 " pdb=" CBI Y01 X1606 " ideal model delta sigma weight residual 1.530 1.172 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" CAK Y01 H2201 " pdb=" CBD Y01 H2201 " ideal model delta sigma weight residual 1.525 1.168 0.357 2.00e-02 2.50e+03 3.18e+02 ... (remaining 7732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 10323 3.27 - 6.55: 175 6.55 - 9.82: 26 9.82 - 13.09: 5 13.09 - 16.37: 5 Bond angle restraints: 10534 Sorted by residual: angle pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" CD PRO H 156 " ideal model delta sigma weight residual 111.50 98.22 13.28 1.40e+00 5.10e-01 9.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 angle pdb=" N SER L 10 " pdb=" CA BSER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4250 17.99 - 35.98: 313 35.98 - 53.97: 98 53.97 - 71.96: 22 71.96 - 89.94: 2 Dihedral angle restraints: 4685 sinusoidal: 1966 harmonic: 2719 Sorted by residual: dihedral pdb=" CA MET X 541 " pdb=" C MET X 541 " pdb=" N LYS X 542 " pdb=" CA LYS X 542 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA TRP X 90 " pdb=" C TRP X 90 " pdb=" N TYR X 91 " pdb=" CA TYR X 91 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 1144 0.315 - 0.631: 12 0.631 - 0.946: 3 0.946 - 1.262: 0 1.262 - 1.577: 3 Chirality restraints: 1162 Sorted by residual: chirality pdb=" CBD Y01 H2201 " pdb=" CAK Y01 H2201 " pdb=" CBF Y01 H2201 " pdb=" CBG Y01 H2201 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" CBD Y01 X1606 " pdb=" CAK Y01 X1606 " pdb=" CBF Y01 X1606 " pdb=" CBG Y01 X1606 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.57 2.00e-01 2.50e+01 6.19e+01 chirality pdb=" CBD Y01 H2202 " pdb=" CAK Y01 H2202 " pdb=" CBF Y01 H2202 " pdb=" CBG Y01 H2202 " both_signs ideal model delta sigma weight residual False 2.70 1.13 1.56 2.00e-01 2.50e+01 6.11e+01 ... (remaining 1159 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 278 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO X 279 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO X 279 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 279 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 193 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO H 194 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 194 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 194 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO X 385 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.020 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 102 2.62 - 3.19: 6680 3.19 - 3.76: 10613 3.76 - 4.33: 16211 4.33 - 4.90: 27373 Nonbonded interactions: 60979 Sorted by model distance: nonbonded pdb=" O LYS X 380 " pdb=" OG1 THR X 381 " model vdw 2.044 3.040 nonbonded pdb=" CE1 TYR H 154 " pdb=" OE2 GLU H 157 " model vdw 2.057 3.340 nonbonded pdb=" O THR H 140 " pdb=" OG SER H 195 " model vdw 2.201 3.040 nonbonded pdb=" O GLN L 126 " pdb=" OG SER L 129 " model vdw 2.201 3.040 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.206 3.120 ... (remaining 60974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.30 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.710 Find NCS groups from input model: 0.070 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:14.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 0.020 0.365 7737 Z= 1.341 Angle : 1.038 16.368 10534 Z= 0.549 Chirality : 0.106 1.577 1162 Planarity : 0.004 0.039 1275 Dihedral : 14.298 89.944 2936 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.23 % Favored : 90.55 % Rotamer: Outliers : 8.07 % Allowed : 8.20 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.23), residues: 917 helix: -2.35 (0.22), residues: 343 sheet: -1.68 (0.35), residues: 193 loop : -3.79 (0.25), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 90 HIS 0.008 0.001 HIS H 35 PHE 0.019 0.001 PHE X 197 TYR 0.016 0.002 TYR L 175 ARG 0.003 0.001 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 0.812 Fit side-chains REVERT: X 98 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8135 (tt) REVERT: X 142 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (mmt) REVERT: X 167 ARG cc_start: 0.7684 (tmm160) cc_final: 0.6745 (mtm110) REVERT: X 473 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (mt) REVERT: H 46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7541 (tt0) REVERT: H 157 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5519 (mp0) outliers start: 65 outliers final: 33 residues processed: 167 average time/residue: 0.8349 time to fit residues: 150.9429 Evaluate side-chains 118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 142 MET Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 343 PHE Chi-restraints excluded: chain X residue 367 SER Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 397 ASP Chi-restraints excluded: chain X residue 430 VAL Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 171 GLN X 317 ASN H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 201 GLN L 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128941 restraints weight = 28667.183| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 5.69 r_work: 0.3214 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7737 Z= 0.212 Angle : 0.649 9.700 10534 Z= 0.328 Chirality : 0.044 0.157 1162 Planarity : 0.006 0.083 1275 Dihedral : 11.849 59.880 1382 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.09 % Allowed : 12.80 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.27), residues: 917 helix: -0.30 (0.28), residues: 343 sheet: -0.83 (0.36), residues: 201 loop : -3.05 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.001 PHE X 343 TYR 0.011 0.001 TYR X 239 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.738 Fit side-chains REVERT: X 98 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8033 (tt) REVERT: X 167 ARG cc_start: 0.7716 (tmm160) cc_final: 0.6870 (ttp-110) REVERT: X 473 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8040 (mt) REVERT: X 530 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: H 46 GLU cc_start: 0.8712 (tt0) cc_final: 0.8479 (tt0) REVERT: H 205 CYS cc_start: 0.2962 (OUTLIER) cc_final: 0.2598 (t) REVERT: L 59 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7869 (Cg_endo) outliers start: 41 outliers final: 19 residues processed: 123 average time/residue: 0.9768 time to fit residues: 129.1615 Evaluate side-chains 104 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 75 HIS X 186 GLN X 291 HIS H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125757 restraints weight = 16609.516| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.48 r_work: 0.3274 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7737 Z= 0.264 Angle : 0.645 9.707 10534 Z= 0.325 Chirality : 0.044 0.148 1162 Planarity : 0.006 0.078 1275 Dihedral : 10.609 59.236 1352 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.98 % Allowed : 15.53 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.28), residues: 917 helix: 0.12 (0.28), residues: 352 sheet: -0.41 (0.37), residues: 201 loop : -2.78 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.006 0.001 HIS H 35 PHE 0.025 0.001 PHE X 343 TYR 0.013 0.001 TYR X 281 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.854 Fit side-chains REVERT: X 98 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8097 (tt) REVERT: X 129 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8203 (ttm170) REVERT: X 167 ARG cc_start: 0.7812 (tmm160) cc_final: 0.7020 (ttp-110) REVERT: X 387 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8089 (tp) REVERT: H 205 CYS cc_start: 0.2931 (OUTLIER) cc_final: 0.2554 (t) REVERT: L 59 PRO cc_start: 0.8193 (Cg_exo) cc_final: 0.7889 (Cg_endo) outliers start: 32 outliers final: 18 residues processed: 114 average time/residue: 1.0401 time to fit residues: 126.8928 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 157 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 = 0.3930 r_free = 0.3930 target = 0.167120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127725 restraints weight = 28803.435| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.73 r_work: 0.3131 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7737 Z= 0.232 Angle : 0.603 8.843 10534 Z= 0.306 Chirality : 0.043 0.148 1162 Planarity : 0.006 0.078 1275 Dihedral : 9.826 59.875 1347 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.85 % Allowed : 15.90 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.28), residues: 917 helix: 0.44 (0.29), residues: 351 sheet: -0.12 (0.38), residues: 200 loop : -2.49 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.024 0.001 PHE X 343 TYR 0.010 0.001 TYR X 239 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.715 Fit side-chains REVERT: X 98 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8068 (tt) REVERT: X 132 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: X 167 ARG cc_start: 0.7886 (tmm160) cc_final: 0.6943 (ttp-110) REVERT: H 205 CYS cc_start: 0.2988 (OUTLIER) cc_final: 0.2604 (t) REVERT: L 24 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7425 (ttm110) REVERT: L 29 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8563 (t) outliers start: 31 outliers final: 20 residues processed: 115 average time/residue: 0.9461 time to fit residues: 117.0504 Evaluate side-chains 108 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 40 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 157 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 = 0.4009 r_free = 0.4009 target = 0.172583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130729 restraints weight = 22987.017| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.51 r_work: 0.3284 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7737 Z= 0.152 Angle : 0.550 7.648 10534 Z= 0.280 Chirality : 0.041 0.149 1162 Planarity : 0.005 0.078 1275 Dihedral : 9.256 57.972 1343 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.23 % Allowed : 17.64 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.29), residues: 917 helix: 0.88 (0.29), residues: 344 sheet: 0.11 (0.38), residues: 200 loop : -2.22 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 PHE 0.021 0.001 PHE X 343 TYR 0.019 0.001 TYR H 154 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.709 Fit side-chains REVERT: X 98 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.7939 (tt) REVERT: X 117 PHE cc_start: 0.8028 (t80) cc_final: 0.7765 (t80) REVERT: X 132 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: X 167 ARG cc_start: 0.7847 (tmm160) cc_final: 0.6888 (ttp-110) REVERT: X 421 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8137 (pttp) REVERT: H 129 SER cc_start: 0.6026 (m) cc_final: 0.5584 (t) outliers start: 26 outliers final: 19 residues processed: 105 average time/residue: 0.9398 time to fit residues: 106.3878 Evaluate side-chains 96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 307 ASP Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 40 optimal weight: 0.0070 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 289 ASN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.172578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130121 restraints weight = 28670.901| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 5.60 r_work: 0.3241 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7737 Z= 0.174 Angle : 0.553 7.863 10534 Z= 0.281 Chirality : 0.041 0.142 1162 Planarity : 0.005 0.080 1275 Dihedral : 9.033 58.123 1341 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.60 % Allowed : 17.76 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 917 helix: 1.04 (0.29), residues: 345 sheet: 0.21 (0.38), residues: 200 loop : -2.09 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.004 0.001 HIS X 425 PHE 0.022 0.001 PHE X 343 TYR 0.011 0.001 TYR H 94 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: X 117 PHE cc_start: 0.7951 (t80) cc_final: 0.7690 (t80) REVERT: X 132 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: X 167 ARG cc_start: 0.7867 (tmm160) cc_final: 0.6839 (ttp-110) REVERT: X 368 MET cc_start: 0.8702 (tpp) cc_final: 0.8470 (mmt) REVERT: X 421 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8101 (pttp) REVERT: X 508 ASP cc_start: 0.8300 (p0) cc_final: 0.7876 (p0) REVERT: X 512 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8297 (mm) REVERT: H 114 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7217 (pt0) REVERT: L 29 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8508 (t) outliers start: 29 outliers final: 20 residues processed: 110 average time/residue: 0.9217 time to fit residues: 109.2900 Evaluate side-chains 98 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 512 LEU Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 378 HIS H 76 ASN L 79 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120574 restraints weight = 25359.122| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.34 r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 7737 Z= 0.521 Angle : 0.751 8.627 10534 Z= 0.382 Chirality : 0.050 0.161 1162 Planarity : 0.006 0.082 1275 Dihedral : 10.043 57.591 1339 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.09 % Allowed : 17.27 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.28), residues: 917 helix: 0.31 (0.28), residues: 353 sheet: -0.07 (0.38), residues: 203 loop : -2.24 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 90 HIS 0.010 0.002 HIS H 35 PHE 0.028 0.002 PHE X 343 TYR 0.020 0.003 TYR X 428 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: X 132 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: X 149 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7922 (m) REVERT: X 167 ARG cc_start: 0.7877 (tmm160) cc_final: 0.6824 (ttp-110) REVERT: X 530 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8685 (m-80) REVERT: L 24 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7390 (ttm110) REVERT: L 29 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (t) outliers start: 41 outliers final: 20 residues processed: 111 average time/residue: 0.9561 time to fit residues: 114.3348 Evaluate side-chains 98 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 149 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain X residue 535 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 119 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 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 = 0.3994 r_free = 0.3994 target = 0.171055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129109 restraints weight = 22933.360| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.60 r_work: 0.3270 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7737 Z= 0.185 Angle : 0.572 7.434 10534 Z= 0.292 Chirality : 0.042 0.149 1162 Planarity : 0.005 0.080 1275 Dihedral : 9.257 58.063 1339 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.11 % Allowed : 19.25 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 917 helix: 0.86 (0.28), residues: 350 sheet: 0.13 (0.38), residues: 200 loop : -2.04 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.006 0.001 HIS X 425 PHE 0.022 0.001 PHE X 343 TYR 0.010 0.001 TYR H 185 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.745 Fit side-chains REVERT: X 117 PHE cc_start: 0.8139 (t80) cc_final: 0.7925 (t80) REVERT: X 132 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: X 167 ARG cc_start: 0.7882 (tmm160) cc_final: 0.6971 (ttp-110) REVERT: X 302 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8536 (ptm-80) REVERT: X 368 MET cc_start: 0.8625 (tpp) cc_final: 0.8398 (mmt) REVERT: H 129 SER cc_start: 0.6045 (m) cc_final: 0.5600 (t) REVERT: L 24 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: L 29 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (t) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 1.0046 time to fit residues: 111.8308 Evaluate side-chains 100 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 119 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.170781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127846 restraints weight = 25001.781| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 5.01 r_work: 0.3228 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 7737 Z= 0.286 Angle : 0.940 59.200 10534 Z= 0.560 Chirality : 0.046 0.445 1162 Planarity : 0.005 0.082 1275 Dihedral : 9.241 58.166 1337 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.23 % Allowed : 19.01 % Favored : 77.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 917 helix: 0.87 (0.28), residues: 350 sheet: 0.12 (0.38), residues: 200 loop : -2.02 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR X 239 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.797 Fit side-chains REVERT: X 132 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: X 167 ARG cc_start: 0.7875 (tmm160) cc_final: 0.6922 (ttp-110) REVERT: X 302 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (ptm-80) REVERT: X 368 MET cc_start: 0.8604 (tpp) cc_final: 0.8381 (mmt) REVERT: H 82 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8740 (mtp) REVERT: H 129 SER cc_start: 0.6102 (m) cc_final: 0.5644 (t) REVERT: L 24 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7453 (ttm110) REVERT: L 29 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (t) outliers start: 26 outliers final: 19 residues processed: 100 average time/residue: 1.0589 time to fit residues: 113.1464 Evaluate side-chains 101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130214 restraints weight = 29370.828| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 5.61 r_work: 0.3199 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 7737 Z= 0.286 Angle : 0.940 59.200 10534 Z= 0.561 Chirality : 0.046 0.445 1162 Planarity : 0.006 0.084 1275 Dihedral : 9.241 58.166 1337 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 19.38 % Favored : 77.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 917 helix: 0.87 (0.28), residues: 350 sheet: 0.12 (0.38), residues: 200 loop : -2.02 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR X 239 ARG 0.006 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.799 Fit side-chains REVERT: X 132 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: X 167 ARG cc_start: 0.7874 (tmm160) cc_final: 0.6854 (ttp-110) REVERT: X 302 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8584 (ptm-80) REVERT: X 368 MET cc_start: 0.8596 (tpp) cc_final: 0.8366 (mmt) REVERT: H 82 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8719 (mtp) REVERT: H 129 SER cc_start: 0.6077 (m) cc_final: 0.5621 (t) REVERT: L 24 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7435 (ttm110) REVERT: L 29 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8551 (t) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 1.0879 time to fit residues: 112.6349 Evaluate side-chains 101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 34 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** 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 = 0.3989 r_free = 0.3989 target = 0.170651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127929 restraints weight = 22084.999| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.50 r_work: 0.3266 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 7737 Z= 0.286 Angle : 0.940 59.200 10534 Z= 0.561 Chirality : 0.046 0.445 1162 Planarity : 0.006 0.084 1275 Dihedral : 9.241 58.166 1337 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 19.38 % Favored : 77.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 917 helix: 0.87 (0.28), residues: 350 sheet: 0.12 (0.38), residues: 200 loop : -2.02 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR X 239 ARG 0.006 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5745.29 seconds wall clock time: 98 minutes 39.18 seconds (5919.18 seconds total)