Starting phenix.real_space_refine on Fri Mar 15 01:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/03_2024/5fn3_3238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/03_2024/5fn3_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_3238/03_2024/5fn3_3238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/03_2024/5fn3_3238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/03_2024/5fn3_3238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/03_2024/5fn3_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.91, 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 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: 1.00 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: 3.15 Time building geometry restraints manager: 4.70 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: 0.270 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: 1.740 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.610 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 : 1.096 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 REVERT: A 50 CYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7372 (p) REVERT: A 95 MET cc_start: 0.9366 (mmt) cc_final: 0.8684 (mmm) REVERT: A 312 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9122 (pp) REVERT: A 326 MET cc_start: 0.9223 (tpt) cc_final: 0.8945 (tmm) REVERT: A 331 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8265 (tp40) REVERT: A 333 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: A 443 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7375 (t0) REVERT: A 554 TYR cc_start: 0.9302 (t80) cc_final: 0.8785 (t80) REVERT: A 574 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 654 LYS cc_start: 0.9010 (pttp) cc_final: 0.8778 (ptpp) REVERT: A 655 ASP cc_start: 0.9191 (m-30) cc_final: 0.8822 (t0) REVERT: B 93 MET cc_start: 0.8994 (mmm) cc_final: 0.8753 (mmm) REVERT: B 117 PRO cc_start: 0.7582 (OUTLIER) cc_final: 0.7116 (Cg_endo) REVERT: B 184 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mm-30) REVERT: B 385 ASP cc_start: 0.8333 (m-30) cc_final: 0.8052 (m-30) REVERT: B 386 PHE cc_start: 0.9085 (t80) cc_final: 0.8459 (t80) REVERT: B 401 SER cc_start: 0.8378 (t) cc_final: 0.8125 (p) REVERT: C 24 THR cc_start: 0.9451 (m) cc_final: 0.9240 (p) REVERT: C 152 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8267 (p0) REVERT: C 178 PHE cc_start: 0.9538 (t80) cc_final: 0.9267 (t80) REVERT: D 23 PHE cc_start: 0.8725 (m-80) cc_final: 0.8167 (m-80) REVERT: D 39 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7302 (tpt170) REVERT: D 49 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9056 (pt0) REVERT: D 66 PHE cc_start: 0.9400 (t80) cc_final: 0.9174 (m-10) REVERT: D 95 THR cc_start: 0.6596 (m) cc_final: 0.6372 (p) outliers start: 125 outliers final: 30 residues processed: 341 average time/residue: 0.1986 time to fit residues: 97.3102 Evaluate side-chains 204 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.6383 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10555 Z= 0.321 Angle : 0.910 12.519 14399 Z= 0.476 Chirality : 0.049 0.314 1678 Planarity : 0.008 0.137 1792 Dihedral : 8.179 65.138 1416 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 1.46 % Allowed : 8.97 % Favored : 89.57 % Rotamer: Outliers : 0.54 % Allowed : 4.99 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 1.04 % 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: 1.88 (0.19), residues: 763 sheet: -2.48 (0.42), residues: 124 loop : -4.08 (0.24), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 247 HIS 0.012 0.002 HIS C 197 PHE 0.033 0.003 PHE B 445 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 226 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 1.089 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: A 95 MET cc_start: 0.9135 (mmt) cc_final: 0.8646 (mmm) REVERT: A 108 MET cc_start: 0.9409 (mmp) cc_final: 0.9144 (mmp) REVERT: A 554 TYR cc_start: 0.8998 (t80) cc_final: 0.8633 (t80) REVERT: A 655 ASP cc_start: 0.9087 (m-30) cc_final: 0.8750 (t0) REVERT: B 106 TYR cc_start: 0.8979 (m-10) cc_final: 0.8469 (m-10) REVERT: B 385 ASP cc_start: 0.8041 (m-30) cc_final: 0.7594 (m-30) REVERT: B 386 PHE cc_start: 0.8835 (t80) cc_final: 0.8496 (t80) REVERT: C 90 TYR cc_start: 0.8747 (t80) cc_final: 0.8350 (t80) REVERT: D 48 THR cc_start: 0.9626 (p) cc_final: 0.9405 (p) outliers start: 6 outliers final: 0 residues processed: 224 average time/residue: 0.1796 time to fit residues: 60.2513 Evaluate side-chains 149 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 220 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 379 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** 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 573 ASN ** 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 8 ASN ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10555 Z= 0.387 Angle : 0.862 12.039 14399 Z= 0.451 Chirality : 0.046 0.323 1678 Planarity : 0.007 0.147 1792 Dihedral : 7.458 54.121 1416 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.43 % Favored : 89.26 % Rotamer: Outliers : 0.27 % Allowed : 3.99 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.80 % 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: -0.90 (0.23), residues: 1304 helix: 1.28 (0.18), residues: 761 sheet: -2.32 (0.45), residues: 116 loop : -3.75 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 247 HIS 0.013 0.002 HIS C 197 PHE 0.034 0.003 PHE A 181 TYR 0.030 0.003 TYR B 115 ARG 0.005 0.001 ARG D 16 *********************** 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 182 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9350 (mmp) cc_final: 0.9036 (mmt) REVERT: B 106 TYR cc_start: 0.8386 (m-10) cc_final: 0.8068 (m-10) REVERT: B 385 ASP cc_start: 0.7989 (m-30) cc_final: 0.7530 (m-30) REVERT: B 386 PHE cc_start: 0.8712 (t80) cc_final: 0.8443 (t80) REVERT: B 414 ILE cc_start: 0.8793 (mt) cc_final: 0.8579 (pt) REVERT: C 178 PHE cc_start: 0.9505 (t80) cc_final: 0.9237 (t80) REVERT: D 95 THR cc_start: 0.5921 (m) cc_final: 0.5239 (m) outliers start: 3 outliers final: 1 residues processed: 181 average time/residue: 0.1898 time to fit residues: 51.6131 Evaluate side-chains 123 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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: 8.9990 chunk 88 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 305 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 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** 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: 0.6463 moved from start: 0.5048 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= 0.226 Angle : 0.775 13.333 14399 Z= 0.399 Chirality : 0.044 0.284 1678 Planarity : 0.006 0.126 1792 Dihedral : 7.003 51.107 1416 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 1.07 % Allowed : 8.13 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % 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: -0.61 (0.24), residues: 1304 helix: 1.44 (0.18), residues: 757 sheet: -2.18 (0.45), residues: 122 loop : -3.42 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 247 HIS 0.011 0.002 HIS C 197 PHE 0.033 0.002 PHE A 302 TYR 0.027 0.002 TYR D 18 ARG 0.004 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 184 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9156 (mmt) cc_final: 0.8469 (tpp) REVERT: A 108 MET cc_start: 0.9369 (mmp) cc_final: 0.9035 (mmt) REVERT: A 364 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 106 TYR cc_start: 0.8082 (m-10) cc_final: 0.7809 (m-10) REVERT: B 385 ASP cc_start: 0.7935 (m-30) cc_final: 0.7436 (m-30) REVERT: B 386 PHE cc_start: 0.8736 (t80) cc_final: 0.8214 (t80) REVERT: B 454 GLN cc_start: 0.9487 (pp30) cc_final: 0.9138 (pp30) REVERT: C 99 GLU cc_start: 0.8484 (pt0) cc_final: 0.8241 (pt0) REVERT: C 178 PHE cc_start: 0.9521 (t80) cc_final: 0.9285 (t80) REVERT: D 95 THR cc_start: 0.5971 (m) cc_final: 0.5075 (m) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1824 time to fit residues: 50.5841 Evaluate side-chains 128 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 9.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 610 HIS ** 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** ** 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: 0.6517 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10555 Z= 0.308 Angle : 0.781 12.023 14399 Z= 0.406 Chirality : 0.043 0.320 1678 Planarity : 0.007 0.128 1792 Dihedral : 6.795 50.408 1416 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % 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: -0.70 (0.23), residues: 1304 helix: 1.29 (0.18), residues: 744 sheet: -1.98 (0.47), residues: 116 loop : -3.22 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 247 HIS 0.010 0.002 HIS C 197 PHE 0.023 0.002 PHE B 465 TYR 0.021 0.002 TYR D 56 ARG 0.008 0.001 ARG A 342 *********************** 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 163 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9417 (mmp) cc_final: 0.9022 (mmt) REVERT: B 385 ASP cc_start: 0.7958 (m-30) cc_final: 0.7466 (m-30) REVERT: B 386 PHE cc_start: 0.8668 (t80) cc_final: 0.8409 (t80) REVERT: C 99 GLU cc_start: 0.8625 (pt0) cc_final: 0.8396 (pt0) REVERT: C 178 PHE cc_start: 0.9466 (t80) cc_final: 0.9196 (t80) REVERT: D 95 THR cc_start: 0.5692 (m) cc_final: 0.4734 (m) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1741 time to fit residues: 43.0525 Evaluate side-chains 118 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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: 2.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 305 GLN A 428 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 573 ASN ** 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 171 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: 0.6538 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10555 Z= 0.301 Angle : 0.776 13.316 14399 Z= 0.403 Chirality : 0.043 0.258 1678 Planarity : 0.006 0.106 1792 Dihedral : 6.681 48.870 1416 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.20 % Favored : 89.80 % Rotamer: Outliers : 0.09 % Allowed : 3.27 % 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: -0.76 (0.23), residues: 1304 helix: 1.21 (0.18), residues: 744 sheet: -2.07 (0.46), residues: 116 loop : -3.17 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 247 HIS 0.014 0.002 HIS C 197 PHE 0.024 0.002 PHE B 86 TYR 0.018 0.002 TYR B 225 ARG 0.009 0.001 ARG A 342 *********************** 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 168 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9462 (mmp) cc_final: 0.9123 (mmp) REVERT: A 347 MET cc_start: 0.9407 (ttt) cc_final: 0.9193 (ttm) REVERT: B 93 MET cc_start: 0.9034 (mmp) cc_final: 0.8828 (mmm) REVERT: B 385 ASP cc_start: 0.7838 (m-30) cc_final: 0.7472 (m-30) REVERT: B 386 PHE cc_start: 0.8728 (t80) cc_final: 0.8420 (t80) REVERT: B 410 CYS cc_start: 0.9713 (m) cc_final: 0.9500 (m) REVERT: C 99 GLU cc_start: 0.8630 (pt0) cc_final: 0.8400 (pt0) REVERT: C 178 PHE cc_start: 0.9421 (t80) cc_final: 0.9091 (t80) REVERT: D 95 THR cc_start: 0.5662 (m) cc_final: 0.4840 (m) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1865 time to fit residues: 46.7349 Evaluate side-chains 121 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 0.0770 chunk 70 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 464 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10555 Z= 0.305 Angle : 0.796 15.845 14399 Z= 0.411 Chirality : 0.044 0.331 1678 Planarity : 0.007 0.154 1792 Dihedral : 6.626 48.708 1416 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.51 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % 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: -0.80 (0.23), residues: 1304 helix: 1.14 (0.18), residues: 745 sheet: -2.22 (0.44), residues: 118 loop : -3.08 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 174 HIS 0.016 0.002 HIS C 197 PHE 0.019 0.002 PHE B 465 TYR 0.022 0.002 TYR A 196 ARG 0.008 0.001 ARG A 342 *********************** 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 163 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9505 (mmp) cc_final: 0.9196 (mmp) REVERT: A 195 CYS cc_start: 0.9163 (m) cc_final: 0.8809 (t) REVERT: A 245 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8828 (pp20) REVERT: B 106 TYR cc_start: 0.8609 (m-80) cc_final: 0.8154 (m-80) REVERT: B 385 ASP cc_start: 0.7863 (m-30) cc_final: 0.7519 (m-30) REVERT: B 386 PHE cc_start: 0.8758 (t80) cc_final: 0.8451 (t80) REVERT: C 99 GLU cc_start: 0.8627 (pt0) cc_final: 0.8383 (pt0) REVERT: C 178 PHE cc_start: 0.9412 (t80) cc_final: 0.9080 (t80) REVERT: D 95 THR cc_start: 0.5280 (m) cc_final: 0.4813 (m) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1851 time to fit residues: 45.3614 Evaluate side-chains 128 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** A 573 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** 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: 0.6524 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10555 Z= 0.233 Angle : 0.759 12.760 14399 Z= 0.392 Chirality : 0.043 0.233 1678 Planarity : 0.006 0.064 1792 Dihedral : 6.528 46.560 1416 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % 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: -0.73 (0.23), residues: 1304 helix: 1.14 (0.18), residues: 748 sheet: -2.25 (0.43), residues: 118 loop : -2.93 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 36 HIS 0.009 0.001 HIS C 171 PHE 0.029 0.002 PHE A 682 TYR 0.018 0.002 TYR C 90 ARG 0.008 0.001 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 178 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9524 (mmp) cc_final: 0.9262 (mmp) REVERT: A 245 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8823 (pp20) REVERT: B 93 MET cc_start: 0.9143 (mmp) cc_final: 0.8912 (mmm) REVERT: B 106 TYR cc_start: 0.8419 (m-80) cc_final: 0.8043 (m-80) REVERT: B 385 ASP cc_start: 0.7824 (m-30) cc_final: 0.7283 (m-30) REVERT: B 386 PHE cc_start: 0.8802 (t80) cc_final: 0.8383 (t80) REVERT: C 99 GLU cc_start: 0.8502 (pt0) cc_final: 0.8239 (pt0) REVERT: C 178 PHE cc_start: 0.9464 (t80) cc_final: 0.9253 (t80) REVERT: D 95 THR cc_start: 0.5670 (m) cc_final: 0.5130 (m) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1809 time to fit residues: 48.7526 Evaluate side-chains 128 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** A 573 ASN ** B 464 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10555 Z= 0.248 Angle : 0.767 12.230 14399 Z= 0.395 Chirality : 0.044 0.225 1678 Planarity : 0.005 0.063 1792 Dihedral : 6.373 45.968 1416 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.90 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % 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: -0.82 (0.23), residues: 1304 helix: 1.05 (0.18), residues: 755 sheet: -2.31 (0.43), residues: 118 loop : -2.99 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 247 HIS 0.009 0.002 HIS C 197 PHE 0.029 0.002 PHE A 181 TYR 0.018 0.002 TYR C 90 ARG 0.005 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 170 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9496 (mmp) cc_final: 0.9191 (mmp) REVERT: A 195 CYS cc_start: 0.8995 (m) cc_final: 0.8701 (t) REVERT: A 245 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8828 (pp20) REVERT: B 106 TYR cc_start: 0.8284 (m-80) cc_final: 0.8039 (m-80) REVERT: B 385 ASP cc_start: 0.7825 (m-30) cc_final: 0.7276 (m-30) REVERT: B 386 PHE cc_start: 0.8777 (t80) cc_final: 0.8437 (t80) REVERT: B 463 HIS cc_start: 0.9393 (m90) cc_final: 0.9066 (m-70) REVERT: C 119 TYR cc_start: 0.8371 (t80) cc_final: 0.8157 (t80) REVERT: C 178 PHE cc_start: 0.9459 (t80) cc_final: 0.9245 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1809 time to fit residues: 46.8560 Evaluate side-chains 130 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 0.0670 chunk 85 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 2.8324 ------------------------------------------------------------------------------- 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 449 HIS ** 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 A 573 ASN ** B 464 GLN ** 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: 0.6563 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10555 Z= 0.256 Angle : 0.758 12.667 14399 Z= 0.390 Chirality : 0.044 0.227 1678 Planarity : 0.005 0.064 1792 Dihedral : 6.273 45.083 1416 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.05 % Favored : 90.03 % 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 : 1.75 % 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: -0.81 (0.23), residues: 1304 helix: 1.04 (0.18), residues: 755 sheet: -2.29 (0.43), residues: 117 loop : -2.96 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 247 HIS 0.010 0.002 HIS C 197 PHE 0.028 0.002 PHE A 181 TYR 0.023 0.002 TYR C 218 ARG 0.006 0.001 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 162 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8731 (tttm) cc_final: 0.8531 (ttpp) REVERT: A 108 MET cc_start: 0.9508 (mmp) cc_final: 0.9205 (mmp) REVERT: A 195 CYS cc_start: 0.9128 (m) cc_final: 0.8785 (t) REVERT: A 245 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8822 (pp20) REVERT: B 93 MET cc_start: 0.9255 (mmp) cc_final: 0.9043 (mmm) REVERT: B 106 TYR cc_start: 0.8206 (m-80) cc_final: 0.7880 (m-80) REVERT: B 386 PHE cc_start: 0.8802 (t80) cc_final: 0.8459 (t80) REVERT: B 463 HIS cc_start: 0.9328 (m90) cc_final: 0.9015 (m90) REVERT: C 119 TYR cc_start: 0.8375 (t80) cc_final: 0.8173 (t80) REVERT: C 128 ILE cc_start: 0.9097 (tp) cc_final: 0.8870 (tp) REVERT: C 178 PHE cc_start: 0.9447 (t80) cc_final: 0.9235 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1619 time to fit residues: 40.2264 Evaluate side-chains 130 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 0.5980 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 444 HIS ** A 449 HIS ** 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 573 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.047467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041353 restraints weight = 80421.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042272 restraints weight = 52566.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042911 restraints weight = 38551.603| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10555 Z= 0.293 Angle : 0.766 12.336 14399 Z= 0.397 Chirality : 0.043 0.218 1678 Planarity : 0.005 0.065 1792 Dihedral : 6.203 45.383 1416 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.51 % Favored : 89.57 % 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 : 0.00 % Twisted General : 0.24 % 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: -0.83 (0.23), residues: 1304 helix: 1.03 (0.18), residues: 748 sheet: -2.25 (0.44), residues: 117 loop : -2.92 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 247 HIS 0.011 0.002 HIS C 197 PHE 0.031 0.002 PHE A 682 TYR 0.020 0.002 TYR A 196 ARG 0.004 0.001 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.41 seconds wall clock time: 37 minutes 27.81 seconds (2247.81 seconds total)