Starting phenix.real_space_refine on Tue Feb 13 16:52:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn5_33311/02_2024/7xn5_33311_updated.pdb" } resolution = 3.18 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 4392 2.51 5 N 1227 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "B ASP 382": "OD1" <-> "OD2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6955 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1791 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'APR': 1, 'NCA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.31, per 1000 atoms: 0.62 Number of scatterers: 6955 At special positions: 0 Unit cell: (106.934, 95.988, 74.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1294 8.00 N 1227 7.00 C 4392 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=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 7 sheets defined 35.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 68 through 79 Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.839A pdb=" N VAL A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 137 through 143 removed outlier: 4.442A pdb=" N PHE A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.522A pdb=" N GLY B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 93 through 111 removed outlier: 4.067A pdb=" N GLN B 97 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B 98 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 109 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.729A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 245 through 250 removed outlier: 4.008A pdb=" N SER B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 279 through 291 removed outlier: 3.614A pdb=" N VAL B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 312 through 315 No H-bonds generated for 'chain 'B' and resid 312 through 315' Processing helix chain 'B' and resid 318 through 321 No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.740A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.552A pdb=" N ASN B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 removed outlier: 3.666A pdb=" N PHE B 399 " --> pdb=" O ALA B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.684A pdb=" N LYS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 136 through 143 removed outlier: 4.499A pdb=" N PHE C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 103 through 110 Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.871A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.078A pdb=" N CYS A 47 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LYS A 88 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 49 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 163 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= D, first strand: chain 'B' and resid 149 through 152 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 Processing sheet with id= F, first strand: chain 'C' and resid 113 through 117 removed outlier: 3.612A pdb=" N LEU C 46 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 49 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 156 through 159 removed outlier: 3.663A pdb=" N CYS C 264 " --> pdb=" O TYR C 197 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 543 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: 1.88 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1161 1.30 - 1.42: 1898 1.42 - 1.55: 3970 1.55 - 1.68: 3 1.68 - 1.81: 66 Bond restraints: 7098 Sorted by residual: bond pdb=" O5D APR B1002 " pdb=" PB APR B1002 " ideal model delta sigma weight residual 1.641 1.519 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" O5' APR B1002 " pdb=" PA APR B1002 " ideal model delta sigma weight residual 1.645 1.527 0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.14e-02 7.69e+03 3.21e+01 bond pdb=" CA GLN B 66 " pdb=" C GLN B 66 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.37e-02 5.33e+03 3.17e+01 bond pdb=" C7 NCA B1001 " pdb=" N7 NCA B1001 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.89e+01 ... (remaining 7093 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.41: 165 106.41 - 113.34: 3747 113.34 - 120.28: 2639 120.28 - 127.21: 2935 127.21 - 134.15: 70 Bond angle restraints: 9556 Sorted by residual: angle pdb=" N LYS B 466 " pdb=" CA LYS B 466 " pdb=" C LYS B 466 " ideal model delta sigma weight residual 114.75 107.80 6.95 1.26e+00 6.30e-01 3.04e+01 angle pdb=" N ALA C 227 " pdb=" CA ALA C 227 " pdb=" C ALA C 227 " ideal model delta sigma weight residual 114.56 109.45 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" O ALA B 65 " pdb=" C ALA B 65 " pdb=" N GLN B 66 " ideal model delta sigma weight residual 122.43 117.24 5.19 1.34e+00 5.57e-01 1.50e+01 angle pdb=" C2D APR B1002 " pdb=" C3D APR B1002 " pdb=" O3D APR B1002 " ideal model delta sigma weight residual 108.38 119.06 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" N ASP A 90 " ideal model delta sigma weight residual 116.39 120.53 -4.14 1.17e+00 7.31e-01 1.25e+01 ... (remaining 9551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3739 17.88 - 35.75: 422 35.75 - 53.63: 67 53.63 - 71.51: 23 71.51 - 89.38: 14 Dihedral angle restraints: 4265 sinusoidal: 1747 harmonic: 2518 Sorted by residual: dihedral pdb=" CA GLU A 190 " pdb=" C GLU A 190 " pdb=" N ALA A 191 " pdb=" CA ALA A 191 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 465 " pdb=" C ILE B 465 " pdb=" N LYS B 466 " pdb=" CA LYS B 466 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1015 0.134 - 0.268: 6 0.268 - 0.403: 0 0.403 - 0.537: 0 0.537 - 0.671: 1 Chirality restraints: 1022 Sorted by residual: chirality pdb=" C3D APR B1002 " pdb=" C2D APR B1002 " pdb=" C4D APR B1002 " pdb=" O3D APR B1002 " both_signs ideal model delta sigma weight residual False -2.71 -2.03 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C4D APR B1002 " pdb=" C3D APR B1002 " pdb=" C5D APR B1002 " pdb=" O4D APR B1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.66 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA GLN B 66 " pdb=" N GLN B 66 " pdb=" C GLN B 66 " pdb=" CB GLN B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1019 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR B1002 " 0.152 2.00e-02 2.50e+03 6.97e-02 1.34e+02 pdb=" C2 APR B1002 " -0.004 2.00e-02 2.50e+03 pdb=" C4 APR B1002 " -0.077 2.00e-02 2.50e+03 pdb=" C5 APR B1002 " -0.072 2.00e-02 2.50e+03 pdb=" C6 APR B1002 " 0.003 2.00e-02 2.50e+03 pdb=" C8 APR B1002 " -0.016 2.00e-02 2.50e+03 pdb=" N1 APR B1002 " 0.037 2.00e-02 2.50e+03 pdb=" N3 APR B1002 " -0.063 2.00e-02 2.50e+03 pdb=" N6 APR B1002 " 0.105 2.00e-02 2.50e+03 pdb=" N7 APR B1002 " -0.047 2.00e-02 2.50e+03 pdb=" N9 APR B1002 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 328 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 329 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C GLN B 66 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN B 66 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 67 " -0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1372 2.77 - 3.31: 6482 3.31 - 3.84: 10991 3.84 - 4.37: 13521 4.37 - 4.90: 23199 Nonbonded interactions: 55565 Sorted by model distance: nonbonded pdb=" OD1 ASP D 122 " pdb=" N GLU D 123 " model vdw 2.242 2.520 nonbonded pdb=" O ARG B 316 " pdb=" OG SER B 320 " model vdw 2.261 2.440 nonbonded pdb=" O LYS C 154 " pdb=" NZ LYS C 156 " model vdw 2.266 2.520 nonbonded pdb=" O ILE D 100 " pdb=" NE2 GLN D 135 " model vdw 2.286 2.520 nonbonded pdb=" O VAL B 303 " pdb=" NE2 GLN B 306 " model vdw 2.288 2.520 ... (remaining 55560 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: 1.870 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: 10.090 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.980 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.005 0.122 7098 Z= 0.272 Angle : 0.693 10.677 9556 Z= 0.386 Chirality : 0.047 0.671 1022 Planarity : 0.005 0.070 1236 Dihedral : 16.223 89.383 2641 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.28), residues: 851 helix: -0.16 (0.29), residues: 330 sheet: -1.15 (0.50), residues: 127 loop : -2.26 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 PHE 0.017 0.001 PHE D 89 TYR 0.005 0.001 TYR C 276 ARG 0.020 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: B 194 GLN cc_start: 0.7943 (mp10) cc_final: 0.7493 (mm-40) REVERT: B 205 MET cc_start: 0.7435 (pmm) cc_final: 0.7224 (ptp) REVERT: C 161 GLN cc_start: 0.8407 (tt0) cc_final: 0.8085 (tt0) REVERT: D 114 GLU cc_start: 0.7502 (mp0) cc_final: 0.7166 (mp0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2008 time to fit residues: 29.7333 Evaluate side-chains 94 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7098 Z= 0.255 Angle : 0.568 7.244 9556 Z= 0.293 Chirality : 0.043 0.177 1022 Planarity : 0.004 0.058 1236 Dihedral : 8.907 85.102 995 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.10 % Allowed : 5.93 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), residues: 851 helix: -0.59 (0.28), residues: 332 sheet: -0.73 (0.52), residues: 124 loop : -2.30 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 261 HIS 0.005 0.001 HIS A 185 PHE 0.015 0.001 PHE B 78 TYR 0.007 0.001 TYR C 195 ARG 0.005 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: B 183 PHE cc_start: 0.8528 (m-10) cc_final: 0.8283 (m-80) REVERT: D 114 GLU cc_start: 0.7371 (mp0) cc_final: 0.7160 (mp0) outliers start: 8 outliers final: 7 residues processed: 105 average time/residue: 0.2046 time to fit residues: 28.3344 Evaluate side-chains 104 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7098 Z= 0.368 Angle : 0.611 7.502 9556 Z= 0.318 Chirality : 0.044 0.163 1022 Planarity : 0.004 0.058 1236 Dihedral : 8.541 81.848 995 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.36 % Rotamer: Outliers : 1.52 % Allowed : 9.79 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.28), residues: 851 helix: -0.95 (0.27), residues: 331 sheet: -0.67 (0.51), residues: 124 loop : -2.32 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.005 0.001 HIS A 185 PHE 0.022 0.002 PHE B 78 TYR 0.008 0.001 TYR C 226 ARG 0.005 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 197 TYR cc_start: 0.7463 (m-80) cc_final: 0.7234 (m-80) REVERT: B 205 MET cc_start: 0.7570 (pmm) cc_final: 0.7297 (ptp) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.2062 time to fit residues: 27.0965 Evaluate side-chains 100 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7098 Z= 0.221 Angle : 0.527 7.041 9556 Z= 0.275 Chirality : 0.041 0.174 1022 Planarity : 0.004 0.055 1236 Dihedral : 8.091 88.902 995 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.93 % Allowed : 12.14 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.28), residues: 851 helix: -0.89 (0.27), residues: 337 sheet: -0.38 (0.53), residues: 121 loop : -2.24 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.014 0.001 PHE B 78 TYR 0.006 0.001 TYR B 302 ARG 0.005 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: C 197 TYR cc_start: 0.7870 (m-80) cc_final: 0.7625 (m-80) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.1914 time to fit residues: 27.2984 Evaluate side-chains 104 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0030 chunk 47 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7098 Z= 0.214 Angle : 0.513 6.852 9556 Z= 0.268 Chirality : 0.041 0.145 1022 Planarity : 0.004 0.054 1236 Dihedral : 7.428 87.365 995 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.21 % Allowed : 12.97 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.28), residues: 851 helix: -0.80 (0.27), residues: 334 sheet: -0.43 (0.52), residues: 124 loop : -2.15 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.003 0.001 HIS A 185 PHE 0.014 0.001 PHE B 78 TYR 0.013 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: C 197 TYR cc_start: 0.7865 (m-80) cc_final: 0.7594 (m-80) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1995 time to fit residues: 28.7972 Evaluate side-chains 105 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7098 Z= 0.352 Angle : 0.586 7.768 9556 Z= 0.305 Chirality : 0.043 0.160 1022 Planarity : 0.004 0.055 1236 Dihedral : 7.314 80.248 995 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.75 % Favored : 90.13 % Rotamer: Outliers : 2.21 % Allowed : 15.17 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.28), residues: 851 helix: -1.03 (0.27), residues: 338 sheet: -0.53 (0.52), residues: 123 loop : -2.24 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.005 0.001 HIS A 185 PHE 0.021 0.002 PHE B 78 TYR 0.018 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.873 Fit side-chains REVERT: B 205 MET cc_start: 0.7588 (pmm) cc_final: 0.7368 (ptp) REVERT: C 197 TYR cc_start: 0.7879 (m-80) cc_final: 0.7669 (m-80) outliers start: 16 outliers final: 15 residues processed: 103 average time/residue: 0.2166 time to fit residues: 29.4622 Evaluate side-chains 106 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7098 Z= 0.161 Angle : 0.500 9.382 9556 Z= 0.260 Chirality : 0.040 0.184 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.741 89.891 995 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.07 % Allowed : 15.59 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.28), residues: 851 helix: -0.55 (0.28), residues: 325 sheet: -0.45 (0.53), residues: 125 loop : -2.10 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 214 HIS 0.002 0.001 HIS D 107 PHE 0.009 0.001 PHE B 78 TYR 0.009 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.832 Fit side-chains REVERT: C 197 TYR cc_start: 0.7848 (m-80) cc_final: 0.7577 (m-80) outliers start: 15 outliers final: 11 residues processed: 107 average time/residue: 0.1941 time to fit residues: 27.8267 Evaluate side-chains 101 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7098 Z= 0.246 Angle : 0.537 9.651 9556 Z= 0.280 Chirality : 0.042 0.147 1022 Planarity : 0.004 0.053 1236 Dihedral : 6.820 83.586 995 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.21 % Allowed : 16.00 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.28), residues: 851 helix: -0.76 (0.28), residues: 333 sheet: -0.51 (0.52), residues: 125 loop : -2.15 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.003 0.001 HIS B 137 PHE 0.016 0.001 PHE B 78 TYR 0.015 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.733 Fit side-chains REVERT: A 61 MET cc_start: 0.6651 (mtt) cc_final: 0.6147 (mtt) REVERT: C 149 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7251 (tpp80) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.2077 time to fit residues: 27.5889 Evaluate side-chains 105 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7098 Z= 0.203 Angle : 0.526 10.514 9556 Z= 0.273 Chirality : 0.041 0.189 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.722 88.133 995 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.34 % Allowed : 16.28 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.28), residues: 851 helix: -0.53 (0.28), residues: 324 sheet: -0.34 (0.53), residues: 123 loop : -2.12 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.003 0.001 HIS A 185 PHE 0.013 0.001 PHE B 78 TYR 0.012 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.856 Fit side-chains REVERT: A 61 MET cc_start: 0.6630 (mtt) cc_final: 0.6092 (mtt) REVERT: C 149 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7238 (tpp80) REVERT: C 197 TYR cc_start: 0.7845 (m-80) cc_final: 0.7614 (m-80) outliers start: 17 outliers final: 15 residues processed: 101 average time/residue: 0.2085 time to fit residues: 28.0852 Evaluate side-chains 106 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7098 Z= 0.176 Angle : 0.512 10.943 9556 Z= 0.265 Chirality : 0.041 0.193 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.561 89.735 995 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.07 % Allowed : 16.69 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 851 helix: -0.43 (0.29), residues: 325 sheet: -0.27 (0.53), residues: 123 loop : -2.10 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.002 0.001 HIS B 202 PHE 0.017 0.001 PHE D 89 TYR 0.010 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.858 Fit side-chains REVERT: C 197 TYR cc_start: 0.7783 (m-80) cc_final: 0.7554 (m-80) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.1924 time to fit residues: 26.1904 Evaluate side-chains 105 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104412 restraints weight = 11295.595| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.76 r_work: 0.3224 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7098 Z= 0.159 Angle : 0.501 10.388 9556 Z= 0.259 Chirality : 0.040 0.212 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.351 87.812 995 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.93 % Allowed : 17.10 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.29), residues: 851 helix: -0.42 (0.29), residues: 329 sheet: -0.10 (0.54), residues: 122 loop : -2.04 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.003 0.001 HIS D 107 PHE 0.009 0.001 PHE B 78 TYR 0.008 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.88 seconds wall clock time: 33 minutes 26.64 seconds (2006.64 seconds total)