Starting phenix.real_space_refine on Tue Jun 25 19:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcm_38247/06_2024/8xcm_38247_updated.pdb" } resolution = 3.08 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= 0.001 sd= 0.014 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5422 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ASP 433": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4168 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 53.333 64.114 34.976 1.00127.49 S ATOM 1738 SG CYS A 222 53.792 68.828 30.722 1.00131.05 S ATOM 1698 SG CYS A 216 52.555 63.628 28.263 1.00131.75 S Time building chain proxies: 5.53, per 1000 atoms: 0.64 Number of scatterers: 8605 At special positions: 0 Unit cell: (104.06, 108.36, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 34.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 93 through 96 removed outlier: 3.556A pdb=" N TYR A 96 " --> pdb=" O ARG A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 139 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.672A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 442 through 461 removed outlier: 3.739A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 523 through 540 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 84 through 100 removed outlier: 4.260A pdb=" N SER B 87 " --> pdb=" O HIS B 84 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 89 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 148 through 153 Proline residue: B 152 - end of helix No H-bonds generated for 'chain 'B' and resid 148 through 153' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.547A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 56' Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.954A pdb=" N HIS C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 265 through 273 Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.848A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 374 through 381 Processing helix chain 'C' and resid 409 through 422 Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing sheet with id= A, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.637A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.501A pdb=" N PHE A 270 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 256 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 329 through 332 removed outlier: 4.358A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 70 through 73 232 hydrogen bonds defined for protein. 627 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: 2.10 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8746 1.76 - 2.30: 90 2.30 - 2.84: 0 2.84 - 3.38: 0 3.38 - 3.92: 3 Bond restraints: 8839 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.922 -1.622 2.00e-02 2.50e+03 6.58e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.801 -1.543 2.00e-02 2.50e+03 5.95e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.708 -1.475 2.00e-02 2.50e+03 5.44e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8834 not shown) Histogram of bond angle deviations from ideal: 38.28 - 66.58: 4 66.58 - 94.89: 20 94.89 - 123.19: 11528 123.19 - 151.50: 525 151.50 - 179.80: 6 Bond angle restraints: 12083 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.86 46.89 3.00e+00 1.11e-01 2.44e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 71.35 41.24 3.00e+00 1.11e-01 1.89e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 67.65 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 38.28 33.47 3.00e+00 1.11e-01 1.24e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 38.78 33.31 3.00e+00 1.11e-01 1.23e+02 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4442 17.92 - 35.84: 588 35.84 - 53.76: 160 53.76 - 71.68: 24 71.68 - 89.60: 13 Dihedral angle restraints: 5227 sinusoidal: 2075 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ALA C 117 " pdb=" C ALA C 117 " pdb=" N MET C 118 " pdb=" CA MET C 118 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 395 " pdb=" C MET C 395 " pdb=" N PRO C 396 " pdb=" CA PRO C 396 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" C2C HEC C 503 " pdb=" C3C HEC C 503 " pdb=" CAC HEC C 503 " pdb=" CBC HEC C 503 " ideal model delta sinusoidal sigma weight residual 60.00 11.00 49.00 2 1.00e+01 1.00e-02 2.73e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.271: 1276 3.271 - 6.543: 0 6.543 - 9.814: 0 9.814 - 13.085: 0 13.085 - 16.356: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -5.59 16.36 2.00e-01 2.50e+01 6.69e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 118 " -0.083 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO B 119 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.022 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" CGD HEC C 501 " 0.082 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 311 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO C 312 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 312 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 312 " 0.055 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 257 2.67 - 3.23: 8972 3.23 - 3.79: 14916 3.79 - 4.34: 20063 4.34 - 4.90: 31841 Nonbonded interactions: 76049 Sorted by model distance: nonbonded pdb=" OH TYR A 79 " pdb=" O GLN A 98 " model vdw 2.118 2.440 nonbonded pdb=" OH TYR A 118 " pdb=" OG SER A 522 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR A 145 " pdb=" OD2 ASP A 535 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.165 2.440 nonbonded pdb=" OD1 ASN A 369 " pdb=" OG1 THR A 371 " model vdw 2.187 2.440 ... (remaining 76044 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 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: 1.910 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: 4.990 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.060 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.030 1.622 8839 Z= 2.203 Angle : 1.333 46.886 12083 Z= 0.534 Chirality : 0.460 16.356 1277 Planarity : 0.007 0.120 1569 Dihedral : 17.720 89.597 3215 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.68 % Allowed : 29.23 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: -0.04 (0.26), residues: 1083 helix: 1.25 (0.28), residues: 375 sheet: -1.91 (0.65), residues: 58 loop : -0.59 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 51 HIS 0.006 0.001 HIS A 110 PHE 0.012 0.001 PHE A 270 TYR 0.023 0.002 TYR A 271 ARG 0.008 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8366 (t0) cc_final: 0.7955 (m-30) REVERT: A 146 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 262 LYS cc_start: 0.9159 (tptp) cc_final: 0.8807 (tppt) REVERT: A 490 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7776 (pmt-80) REVERT: B 141 VAL cc_start: 0.8530 (t) cc_final: 0.8256 (p) REVERT: B 169 TYR cc_start: 0.9015 (p90) cc_final: 0.8719 (p90) REVERT: C 120 TYR cc_start: 0.8736 (p90) cc_final: 0.8387 (p90) REVERT: C 172 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7719 (mmt-90) outliers start: 6 outliers final: 2 residues processed: 144 average time/residue: 0.2126 time to fit residues: 42.1762 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 332 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 8839 Z= 0.356 Angle : 1.106 84.284 12083 Z= 0.432 Chirality : 0.065 1.669 1277 Planarity : 0.006 0.057 1569 Dihedral : 8.968 79.083 1288 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.95 % Allowed : 25.17 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.03 (0.26), residues: 1083 helix: 1.28 (0.28), residues: 369 sheet: -1.11 (0.60), residues: 68 loop : -0.59 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.017 0.002 PHE A 80 TYR 0.018 0.002 TYR A 271 ARG 0.006 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8880 (mtp) cc_final: 0.8485 (mtp) REVERT: A 262 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8854 (tppp) REVERT: A 266 THR cc_start: 0.8687 (m) cc_final: 0.8423 (p) REVERT: A 456 MET cc_start: 0.8710 (mmm) cc_final: 0.8478 (tpp) REVERT: A 490 ARG cc_start: 0.8543 (ptt-90) cc_final: 0.8029 (pmt-80) REVERT: B 141 VAL cc_start: 0.8563 (t) cc_final: 0.8299 (p) REVERT: C 118 MET cc_start: 0.8818 (tpt) cc_final: 0.8033 (tpt) REVERT: C 395 MET cc_start: 0.8597 (tpt) cc_final: 0.8048 (tpt) REVERT: C 410 GLU cc_start: 0.8601 (tp30) cc_final: 0.8363 (tp30) outliers start: 35 outliers final: 21 residues processed: 147 average time/residue: 0.2034 time to fit residues: 41.7257 Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8839 Z= 0.247 Angle : 1.047 83.027 12083 Z= 0.402 Chirality : 0.060 1.504 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.547 81.819 1287 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.84 % Allowed : 24.60 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.07 (0.26), residues: 1083 helix: 1.21 (0.28), residues: 381 sheet: -1.10 (0.61), residues: 70 loop : -0.52 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.027 0.002 PHE B 86 TYR 0.017 0.001 TYR A 271 ARG 0.004 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8541 (t0) cc_final: 0.8048 (m-30) REVERT: A 156 MET cc_start: 0.8728 (mtp) cc_final: 0.8311 (mtp) REVERT: A 262 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8979 (tppp) REVERT: A 266 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 285 PHE cc_start: 0.7679 (m-80) cc_final: 0.7458 (m-80) REVERT: A 456 MET cc_start: 0.8742 (mmm) cc_final: 0.8527 (tpp) REVERT: A 490 ARG cc_start: 0.8614 (ptt-90) cc_final: 0.8082 (pmt-80) REVERT: B 49 ASP cc_start: 0.8329 (m-30) cc_final: 0.8025 (t0) REVERT: B 141 VAL cc_start: 0.8588 (t) cc_final: 0.8294 (p) REVERT: B 180 MET cc_start: 0.8827 (mmm) cc_final: 0.8608 (mmm) REVERT: C 118 MET cc_start: 0.8794 (tpt) cc_final: 0.7913 (tpt) REVERT: C 395 MET cc_start: 0.8378 (tpt) cc_final: 0.8110 (tpt) REVERT: C 410 GLU cc_start: 0.8717 (tp30) cc_final: 0.8493 (tp30) outliers start: 34 outliers final: 21 residues processed: 156 average time/residue: 0.2049 time to fit residues: 44.7044 Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8839 Z= 0.239 Angle : 1.045 83.150 12083 Z= 0.400 Chirality : 0.060 1.488 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.448 82.537 1287 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.30 % Allowed : 24.38 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.12 (0.26), residues: 1083 helix: 1.23 (0.28), residues: 382 sheet: -0.93 (0.61), residues: 74 loop : -0.49 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.017 0.001 PHE B 86 TYR 0.016 0.001 TYR A 271 ARG 0.003 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 156 MET cc_start: 0.8801 (mtp) cc_final: 0.8376 (mtp) REVERT: A 171 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8760 (p0) REVERT: A 175 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7084 (mmt) REVERT: A 262 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8994 (tppp) REVERT: A 266 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (p) REVERT: A 285 PHE cc_start: 0.7671 (m-80) cc_final: 0.7421 (m-80) REVERT: A 305 ARG cc_start: 0.8444 (tpt90) cc_final: 0.7427 (ttm110) REVERT: B 49 ASP cc_start: 0.8329 (m-30) cc_final: 0.8030 (t0) REVERT: B 141 VAL cc_start: 0.8631 (t) cc_final: 0.8360 (p) REVERT: C 118 MET cc_start: 0.8826 (tpt) cc_final: 0.8167 (tpt) REVERT: C 395 MET cc_start: 0.8387 (tpt) cc_final: 0.8001 (tpt) REVERT: C 410 GLU cc_start: 0.8719 (tp30) cc_final: 0.8483 (tp30) outliers start: 47 outliers final: 30 residues processed: 155 average time/residue: 0.1982 time to fit residues: 43.0652 Evaluate side-chains 150 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 8839 Z= 0.337 Angle : 1.072 83.373 12083 Z= 0.413 Chirality : 0.061 1.488 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.627 84.210 1287 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.64 % Allowed : 23.59 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.10 (0.26), residues: 1083 helix: 1.23 (0.28), residues: 381 sheet: -0.80 (0.66), residues: 68 loop : -0.54 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 503 PHE 0.018 0.001 PHE A 80 TYR 0.015 0.001 TYR A 271 ARG 0.003 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 118 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9030 (tp) cc_final: 0.8758 (tp) REVERT: A 57 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 156 MET cc_start: 0.8848 (mtp) cc_final: 0.8437 (mtp) REVERT: A 171 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8686 (p0) REVERT: A 175 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6920 (mmt) REVERT: A 266 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 305 ARG cc_start: 0.8565 (tpt90) cc_final: 0.7465 (ttm110) REVERT: A 490 ARG cc_start: 0.8826 (ptt-90) cc_final: 0.8146 (pmt-80) REVERT: A 535 ASP cc_start: 0.8379 (t0) cc_final: 0.7852 (m-30) REVERT: B 49 ASP cc_start: 0.8339 (m-30) cc_final: 0.8051 (t0) REVERT: B 104 ASP cc_start: 0.8527 (m-30) cc_final: 0.7502 (p0) REVERT: B 136 GLU cc_start: 0.8896 (pm20) cc_final: 0.8596 (pm20) REVERT: B 141 VAL cc_start: 0.8742 (t) cc_final: 0.8433 (p) REVERT: C 118 MET cc_start: 0.8902 (tpt) cc_final: 0.8080 (tpt) REVERT: C 395 MET cc_start: 0.8627 (tpt) cc_final: 0.8106 (tpt) REVERT: C 410 GLU cc_start: 0.8735 (tp30) cc_final: 0.8469 (tp30) outliers start: 50 outliers final: 37 residues processed: 151 average time/residue: 0.2043 time to fit residues: 42.9758 Evaluate side-chains 151 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8839 Z= 0.246 Angle : 1.044 83.270 12083 Z= 0.398 Chirality : 0.060 1.473 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.368 86.029 1287 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.97 % Allowed : 24.15 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.15 (0.26), residues: 1083 helix: 1.24 (0.28), residues: 383 sheet: -0.94 (0.61), residues: 74 loop : -0.46 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.015 0.001 PHE B 60 TYR 0.015 0.001 TYR A 271 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9026 (tp) cc_final: 0.8730 (tp) REVERT: A 171 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8707 (p0) REVERT: A 175 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7166 (mmt) REVERT: A 265 ILE cc_start: 0.7225 (pt) cc_final: 0.6886 (pt) REVERT: A 266 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 305 ARG cc_start: 0.8636 (tpt90) cc_final: 0.7572 (ttm110) REVERT: A 535 ASP cc_start: 0.8411 (t0) cc_final: 0.7882 (m-30) REVERT: B 49 ASP cc_start: 0.8279 (m-30) cc_final: 0.8004 (t70) REVERT: B 104 ASP cc_start: 0.8518 (m-30) cc_final: 0.7452 (p0) REVERT: B 136 GLU cc_start: 0.8909 (pm20) cc_final: 0.8601 (pm20) REVERT: C 118 MET cc_start: 0.8902 (tpt) cc_final: 0.8111 (tpt) REVERT: C 161 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8155 (mtp85) REVERT: C 182 HIS cc_start: 0.8998 (m90) cc_final: 0.8790 (m-70) REVERT: C 395 MET cc_start: 0.8450 (tpt) cc_final: 0.7938 (tpt) REVERT: C 410 GLU cc_start: 0.8769 (tp30) cc_final: 0.8500 (tp30) outliers start: 44 outliers final: 31 residues processed: 148 average time/residue: 0.1838 time to fit residues: 39.0073 Evaluate side-chains 147 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8839 Z= 0.211 Angle : 1.037 83.253 12083 Z= 0.392 Chirality : 0.059 1.467 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.176 86.443 1287 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.63 % Allowed : 24.72 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.07 (0.26), residues: 1083 helix: 1.12 (0.28), residues: 391 sheet: -0.91 (0.61), residues: 74 loop : -0.50 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.014 0.001 PHE B 86 TYR 0.014 0.001 TYR A 271 ARG 0.005 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8575 (t0) cc_final: 0.8031 (m-30) REVERT: A 171 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 175 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7295 (mmt) REVERT: A 266 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 305 ARG cc_start: 0.8683 (tpt90) cc_final: 0.7571 (ttm110) REVERT: A 477 GLN cc_start: 0.8724 (mp10) cc_final: 0.8223 (mp10) REVERT: A 535 ASP cc_start: 0.8437 (t0) cc_final: 0.7958 (m-30) REVERT: B 49 ASP cc_start: 0.8259 (m-30) cc_final: 0.7951 (t70) REVERT: B 87 SER cc_start: 0.8783 (m) cc_final: 0.8486 (p) REVERT: B 104 ASP cc_start: 0.8472 (m-30) cc_final: 0.7452 (p0) REVERT: B 177 VAL cc_start: 0.8972 (m) cc_final: 0.8682 (t) REVERT: C 118 MET cc_start: 0.8831 (tpt) cc_final: 0.8084 (tpt) REVERT: C 182 HIS cc_start: 0.8993 (m90) cc_final: 0.8779 (m-70) REVERT: C 395 MET cc_start: 0.7993 (tpt) cc_final: 0.7466 (tpt) REVERT: C 410 GLU cc_start: 0.8797 (tp30) cc_final: 0.8457 (tp30) outliers start: 41 outliers final: 33 residues processed: 154 average time/residue: 0.1869 time to fit residues: 41.4113 Evaluate side-chains 157 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.0670 chunk 62 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 0.0470 chunk 99 optimal weight: 0.9980 overall best weight: 0.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 433 HIS B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8839 Z= 0.199 Angle : 1.033 83.368 12083 Z= 0.390 Chirality : 0.058 1.451 1277 Planarity : 0.005 0.062 1569 Dihedral : 7.976 86.282 1287 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.40 % Allowed : 24.72 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.16 (0.26), residues: 1083 helix: 1.18 (0.27), residues: 390 sheet: -0.69 (0.61), residues: 73 loop : -0.46 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.017 0.001 PHE B 60 TYR 0.014 0.001 TYR A 271 ARG 0.006 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8931 (t0) cc_final: 0.8577 (t0) REVERT: A 171 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8699 (p0) REVERT: A 175 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7436 (mmt) REVERT: A 258 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 266 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 305 ARG cc_start: 0.8710 (tpt90) cc_final: 0.7463 (ttm110) REVERT: A 479 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7867 (mt) REVERT: A 535 ASP cc_start: 0.8462 (t0) cc_final: 0.7999 (m-30) REVERT: B 49 ASP cc_start: 0.8189 (m-30) cc_final: 0.7905 (t70) REVERT: B 177 VAL cc_start: 0.9009 (m) cc_final: 0.8739 (t) REVERT: C 118 MET cc_start: 0.8680 (tpt) cc_final: 0.8032 (tpt) REVERT: C 182 HIS cc_start: 0.8987 (m90) cc_final: 0.8769 (m-70) REVERT: C 395 MET cc_start: 0.7512 (tpt) cc_final: 0.6925 (tpt) REVERT: C 410 GLU cc_start: 0.8828 (tp30) cc_final: 0.8479 (tp30) outliers start: 39 outliers final: 27 residues processed: 175 average time/residue: 0.1893 time to fit residues: 46.5966 Evaluate side-chains 163 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8839 Z= 0.231 Angle : 1.046 83.116 12083 Z= 0.398 Chirality : 0.059 1.479 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.053 85.738 1287 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.18 % Allowed : 26.30 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.24 (0.26), residues: 1083 helix: 1.23 (0.28), residues: 385 sheet: -0.60 (0.62), residues: 73 loop : -0.39 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.006 0.001 HIS A 110 PHE 0.015 0.001 PHE B 86 TYR 0.014 0.001 TYR A 271 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8922 (t0) cc_final: 0.8577 (t0) REVERT: A 171 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8687 (p0) REVERT: A 175 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7407 (mmt) REVERT: A 258 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: A 266 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8085 (p) REVERT: A 305 ARG cc_start: 0.8706 (tpt90) cc_final: 0.7551 (ttm110) REVERT: A 535 ASP cc_start: 0.8496 (t0) cc_final: 0.8042 (m-30) REVERT: B 49 ASP cc_start: 0.8188 (m-30) cc_final: 0.7906 (t70) REVERT: B 134 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 177 VAL cc_start: 0.8993 (m) cc_final: 0.8726 (t) REVERT: C 118 MET cc_start: 0.8802 (tpt) cc_final: 0.8122 (tpt) REVERT: C 182 HIS cc_start: 0.8995 (m90) cc_final: 0.8786 (m-70) REVERT: C 203 GLU cc_start: 0.8935 (tp30) cc_final: 0.8616 (tp30) REVERT: C 395 MET cc_start: 0.7847 (tpt) cc_final: 0.7157 (tpt) REVERT: C 410 GLU cc_start: 0.8838 (tp30) cc_final: 0.8486 (tp30) outliers start: 37 outliers final: 26 residues processed: 156 average time/residue: 0.1695 time to fit residues: 39.0176 Evaluate side-chains 158 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.0070 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 0.0030 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8839 Z= 0.226 Angle : 1.046 83.181 12083 Z= 0.398 Chirality : 0.059 1.473 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.014 85.994 1287 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.61 % Allowed : 26.64 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.24 (0.26), residues: 1083 helix: 1.16 (0.27), residues: 391 sheet: -0.59 (0.62), residues: 75 loop : -0.35 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.019 0.001 PHE B 60 TYR 0.015 0.001 TYR A 271 ARG 0.005 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8889 (t0) cc_final: 0.8507 (t0) REVERT: A 171 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8676 (p0) REVERT: A 175 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7424 (mmt) REVERT: A 266 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 305 ARG cc_start: 0.8718 (tpt90) cc_final: 0.7583 (ttm110) REVERT: A 535 ASP cc_start: 0.8498 (t0) cc_final: 0.8065 (m-30) REVERT: B 49 ASP cc_start: 0.8149 (m-30) cc_final: 0.7866 (t70) REVERT: B 136 GLU cc_start: 0.8972 (pm20) cc_final: 0.8683 (pm20) REVERT: B 177 VAL cc_start: 0.9001 (m) cc_final: 0.8713 (t) REVERT: C 118 MET cc_start: 0.8732 (tpt) cc_final: 0.8046 (tpt) REVERT: C 182 HIS cc_start: 0.8989 (m90) cc_final: 0.8785 (m-70) REVERT: C 328 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (t) REVERT: C 395 MET cc_start: 0.7816 (tpt) cc_final: 0.7126 (tpt) REVERT: C 410 GLU cc_start: 0.8830 (tp30) cc_final: 0.8486 (tp30) outliers start: 32 outliers final: 23 residues processed: 150 average time/residue: 0.1719 time to fit residues: 38.4731 Evaluate side-chains 147 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.0020 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 124 ASN ** 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 = 0.3325 r_free = 0.3325 target = 0.091498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074484 restraints weight = 17413.013| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.08 r_work: 0.2916 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8839 Z= 0.247 Angle : 1.048 83.060 12083 Z= 0.402 Chirality : 0.060 1.484 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.124 86.166 1287 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.84 % Allowed : 26.64 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.20 (0.27), residues: 1083 helix: 1.16 (0.27), residues: 391 sheet: -1.02 (0.59), residues: 80 loop : -0.33 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.015 0.001 PHE B 86 TYR 0.015 0.001 TYR A 271 ARG 0.004 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.42 seconds wall clock time: 39 minutes 16.57 seconds (2356.57 seconds total)