Starting phenix.real_space_refine on Thu Mar 14 21:55:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blw_16114/03_2024/8blw_16114_updated.pdb" } resolution = 3.22 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6239 2.51 5 N 1683 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9883 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4974 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4898 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 23, 'TRANS': 602} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 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: 5.66, per 1000 atoms: 0.57 Number of scatterers: 9883 At special positions: 0 Unit cell: (81.9, 71.89, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1943 8.00 N 1683 7.00 C 6239 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 18 sheets defined 3.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.708A pdb=" N LYS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 80' Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing sheet with id= A, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.807A pdb=" N GLN A 164 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 138 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 162 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 140 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 160 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 85 through 87 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 removed outlier: 3.659A pdb=" N TYR A 495 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 442 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 362 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 193 through 199 removed outlier: 4.443A pdb=" N GLU A 244 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 272 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 254 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 321 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 222 through 224 Processing sheet with id= F, first strand: chain 'A' and resid 295 through 304 Processing sheet with id= G, first strand: chain 'A' and resid 511 through 515 Processing sheet with id= H, first strand: chain 'A' and resid 530 through 532 Processing sheet with id= I, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= J, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.697A pdb=" N ILE B 128 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 140 through 145 removed outlier: 6.829A pdb=" N CYS B 153 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE B 143 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 151 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 145 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 171 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 163 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 169 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 182 through 185 removed outlier: 3.873A pdb=" N THR B 207 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 220 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 212 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 231 through 234 removed outlier: 4.269A pdb=" N ALA B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 259 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.366A pdb=" N GLY B 365 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 348 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP B 363 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS B 350 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU B 361 " --> pdb=" O CYS B 350 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.530A pdb=" N GLU B 401 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 466 through 468 Processing sheet with id= R, first strand: chain 'B' and resid 571 through 576 removed outlier: 3.953A pdb=" N ARG B 540 " --> pdb=" O TYR B 530 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3204 1.34 - 1.46: 2285 1.46 - 1.58: 4584 1.58 - 1.70: 1 1.70 - 1.82: 29 Bond restraints: 10103 Sorted by residual: bond pdb=" CG PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.69e+01 bond pdb=" C5 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.412 1.481 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CB PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.75e+00 bond pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.26e+00 bond pdb=" C1 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.407 1.451 -0.044 2.00e-02 2.50e+03 4.93e+00 ... (remaining 10098 not shown) Histogram of bond angle deviations from ideal: 92.83 - 101.08: 14 101.08 - 109.33: 1049 109.33 - 117.58: 6252 117.58 - 125.83: 6218 125.83 - 134.08: 186 Bond angle restraints: 13719 Sorted by residual: angle pdb=" CA PRO A 175 " pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 112.00 94.52 17.48 1.40e+00 5.10e-01 1.56e+02 angle pdb=" N PRO A 175 " pdb=" CD PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 103.20 92.83 10.37 1.50e+00 4.44e-01 4.78e+01 angle pdb=" C LYS B 147 " pdb=" N ASP B 148 " pdb=" CA ASP B 148 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C GLN B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 122.46 129.32 -6.86 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N VAL B 44 " pdb=" CA VAL B 44 " pdb=" C VAL B 44 " ideal model delta sigma weight residual 106.21 111.38 -5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 5612 22.45 - 44.90: 312 44.90 - 67.35: 30 67.35 - 89.80: 15 89.80 - 112.26: 3 Dihedral angle restraints: 5972 sinusoidal: 2339 harmonic: 3633 Sorted by residual: dihedral pdb=" CA GLN B 533 " pdb=" C GLN B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ARG A 454 " pdb=" C ARG A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 550 " pdb=" C PHE B 550 " pdb=" N VAL B 551 " pdb=" CA VAL B 551 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1266 0.085 - 0.171: 198 0.171 - 0.256: 24 0.256 - 0.341: 0 0.341 - 0.427: 1 Chirality restraints: 1489 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1486 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 174 " -0.127 5.00e-02 4.00e+02 1.75e-01 4.90e+01 pdb=" N PRO A 175 " 0.302 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 213 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C MET A 213 " 0.058 2.00e-02 2.50e+03 pdb=" O MET A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 214 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 551 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C ILE A 551 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 551 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.016 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2137 2.79 - 3.31: 8695 3.31 - 3.84: 16886 3.84 - 4.37: 19484 4.37 - 4.90: 34584 Nonbonded interactions: 81786 Sorted by model distance: nonbonded pdb=" O ALA A 82 " pdb=" OG1 THR A 558 " model vdw 2.257 2.440 nonbonded pdb=" OG SER B 324 " pdb=" O ASN B 369 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR A 598 " pdb=" O LEU A 601 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR B 284 " pdb=" OE1 GLN B 353 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR B 478 " pdb=" O THR B 480 " model vdw 2.308 2.440 ... (remaining 81781 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.830 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.670 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.156 10103 Z= 0.373 Angle : 1.048 17.481 13719 Z= 0.577 Chirality : 0.063 0.427 1489 Planarity : 0.008 0.175 1796 Dihedral : 14.225 112.256 3656 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -1.93 (0.23), residues: 1238 helix: -2.85 (0.55), residues: 50 sheet: -0.41 (0.23), residues: 536 loop : -1.94 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 590 HIS 0.014 0.002 HIS A 80 PHE 0.035 0.003 PHE B 216 TYR 0.034 0.003 TYR A 395 ARG 0.014 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.885 Fit side-chains REVERT: A 113 ASP cc_start: 0.7168 (t70) cc_final: 0.6868 (t0) REVERT: B 369 ASN cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: B 429 HIS cc_start: 0.7729 (m-70) cc_final: 0.7399 (m170) REVERT: B 508 TRP cc_start: 0.7598 (m100) cc_final: 0.6735 (m100) REVERT: B 597 TRP cc_start: 0.8764 (p-90) cc_final: 0.7910 (p-90) REVERT: B 616 TRP cc_start: 0.8423 (m-10) cc_final: 0.8195 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1608 time to fit residues: 26.8179 Evaluate side-chains 71 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0010 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10103 Z= 0.186 Angle : 0.559 7.145 13719 Z= 0.298 Chirality : 0.046 0.213 1489 Planarity : 0.004 0.074 1796 Dihedral : 5.321 26.829 1390 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.03 % Allowed : 7.60 % Favored : 91.37 % 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: -1.72 (0.23), residues: 1238 helix: -1.78 (0.67), residues: 50 sheet: -0.44 (0.23), residues: 539 loop : -1.71 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 399 HIS 0.002 0.001 HIS B 254 PHE 0.018 0.001 PHE A 311 TYR 0.022 0.001 TYR A 269 ARG 0.007 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7391 (t70) cc_final: 0.7049 (t0) REVERT: A 304 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 429 HIS cc_start: 0.8076 (m-70) cc_final: 0.7801 (m170) REVERT: B 508 TRP cc_start: 0.7558 (m100) cc_final: 0.6845 (m100) REVERT: B 597 TRP cc_start: 0.8785 (p-90) cc_final: 0.7824 (p-90) REVERT: B 616 TRP cc_start: 0.8467 (m-10) cc_final: 0.8135 (m-10) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.1768 time to fit residues: 25.2306 Evaluate side-chains 80 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10103 Z= 0.287 Angle : 0.591 9.056 13719 Z= 0.312 Chirality : 0.047 0.235 1489 Planarity : 0.004 0.085 1796 Dihedral : 5.095 26.594 1390 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.78 % Allowed : 9.38 % Favored : 88.84 % 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: -1.74 (0.24), residues: 1238 helix: -1.56 (0.65), residues: 55 sheet: -0.62 (0.23), residues: 539 loop : -1.57 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 399 HIS 0.003 0.001 HIS A 631 PHE 0.020 0.002 PHE A 520 TYR 0.021 0.002 TYR A 269 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7715 (t70) cc_final: 0.7426 (t0) REVERT: A 363 LEU cc_start: 0.8624 (tp) cc_final: 0.8309 (tt) REVERT: A 460 ASP cc_start: 0.8439 (m-30) cc_final: 0.8182 (m-30) REVERT: B 419 ASP cc_start: 0.8861 (m-30) cc_final: 0.8522 (p0) REVERT: B 508 TRP cc_start: 0.7552 (m100) cc_final: 0.6778 (m100) REVERT: B 541 TRP cc_start: 0.8060 (p-90) cc_final: 0.7577 (p-90) REVERT: B 597 TRP cc_start: 0.8785 (p-90) cc_final: 0.7854 (p-90) REVERT: B 616 TRP cc_start: 0.8532 (m-10) cc_final: 0.8238 (m-10) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.1694 time to fit residues: 25.2533 Evaluate side-chains 85 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 306 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10103 Z= 0.334 Angle : 0.598 10.888 13719 Z= 0.315 Chirality : 0.047 0.218 1489 Planarity : 0.004 0.040 1796 Dihedral : 5.113 23.485 1390 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.91 % Allowed : 10.98 % Favored : 86.12 % 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: -1.74 (0.24), residues: 1238 helix: -1.38 (0.68), residues: 55 sheet: -0.71 (0.23), residues: 540 loop : -1.49 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.003 0.001 HIS A 631 PHE 0.018 0.002 PHE A 296 TYR 0.021 0.002 TYR A 269 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7774 (t70) cc_final: 0.7475 (t0) REVERT: A 363 LEU cc_start: 0.8630 (tp) cc_final: 0.8292 (tt) REVERT: A 460 ASP cc_start: 0.8480 (m-30) cc_final: 0.8183 (m-30) REVERT: B 419 ASP cc_start: 0.8942 (m-30) cc_final: 0.8712 (p0) REVERT: B 508 TRP cc_start: 0.7538 (m100) cc_final: 0.6733 (m100) REVERT: B 524 ASN cc_start: 0.8590 (t0) cc_final: 0.8360 (t0) REVERT: B 541 TRP cc_start: 0.8113 (p-90) cc_final: 0.7664 (p-90) outliers start: 31 outliers final: 19 residues processed: 95 average time/residue: 0.1590 time to fit residues: 24.2915 Evaluate side-chains 88 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.222 Angle : 0.554 9.317 13719 Z= 0.291 Chirality : 0.046 0.233 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.858 22.180 1390 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.47 % Allowed : 10.69 % Favored : 85.83 % 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: -1.67 (0.24), residues: 1238 helix: -1.25 (0.69), residues: 55 sheet: -0.69 (0.23), residues: 538 loop : -1.41 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 616 HIS 0.002 0.000 HIS B 254 PHE 0.016 0.001 PHE A 296 TYR 0.020 0.001 TYR A 269 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 77 time to evaluate : 1.131 Fit side-chains REVERT: A 113 ASP cc_start: 0.7696 (t70) cc_final: 0.7385 (t0) REVERT: A 460 ASP cc_start: 0.8467 (m-30) cc_final: 0.8169 (m-30) REVERT: B 366 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7555 (tp) REVERT: B 508 TRP cc_start: 0.7473 (m100) cc_final: 0.6687 (m100) REVERT: B 524 ASN cc_start: 0.8663 (t0) cc_final: 0.8424 (t0) REVERT: B 541 TRP cc_start: 0.8061 (p-90) cc_final: 0.7639 (p-90) REVERT: B 597 TRP cc_start: 0.8685 (p-90) cc_final: 0.7740 (p-90) REVERT: B 616 TRP cc_start: 0.8670 (m-10) cc_final: 0.8306 (m-10) outliers start: 37 outliers final: 27 residues processed: 104 average time/residue: 0.1526 time to fit residues: 25.9908 Evaluate side-chains 94 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10103 Z= 0.192 Angle : 0.543 8.687 13719 Z= 0.286 Chirality : 0.046 0.220 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.718 20.376 1390 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.56 % Allowed : 11.73 % Favored : 84.71 % 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: -1.56 (0.24), residues: 1238 helix: -1.17 (0.71), residues: 55 sheet: -0.64 (0.23), residues: 538 loop : -1.31 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 387 HIS 0.002 0.000 HIS B 254 PHE 0.016 0.001 PHE A 296 TYR 0.025 0.001 TYR A 636 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 74 time to evaluate : 1.153 Fit side-chains REVERT: A 113 ASP cc_start: 0.7710 (t70) cc_final: 0.7478 (t70) REVERT: A 460 ASP cc_start: 0.8462 (m-30) cc_final: 0.8168 (m-30) REVERT: B 366 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7567 (tp) REVERT: B 508 TRP cc_start: 0.7432 (m100) cc_final: 0.6664 (m100) REVERT: B 524 ASN cc_start: 0.8698 (t0) cc_final: 0.8445 (t0) REVERT: B 541 TRP cc_start: 0.8077 (p-90) cc_final: 0.7668 (p-90) REVERT: B 597 TRP cc_start: 0.8683 (p-90) cc_final: 0.7734 (p-90) REVERT: B 616 TRP cc_start: 0.8663 (m-10) cc_final: 0.8312 (m-10) outliers start: 38 outliers final: 28 residues processed: 101 average time/residue: 0.1879 time to fit residues: 29.0650 Evaluate side-chains 96 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 322 GLN A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10103 Z= 0.296 Angle : 0.590 9.539 13719 Z= 0.309 Chirality : 0.047 0.251 1489 Planarity : 0.004 0.039 1796 Dihedral : 4.869 23.007 1390 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.75 % Allowed : 12.01 % Favored : 84.24 % 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: -1.67 (0.24), residues: 1238 helix: -1.18 (0.70), residues: 55 sheet: -0.83 (0.23), residues: 545 loop : -1.28 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 387 HIS 0.003 0.001 HIS A 631 PHE 0.018 0.001 PHE A 296 TYR 0.022 0.002 TYR A 269 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 71 time to evaluate : 1.171 Fit side-chains REVERT: A 219 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: B 508 TRP cc_start: 0.7417 (m100) cc_final: 0.6641 (m100) REVERT: B 524 ASN cc_start: 0.8789 (t0) cc_final: 0.8486 (t0) REVERT: B 597 TRP cc_start: 0.8678 (p-90) cc_final: 0.7715 (p-90) REVERT: B 616 TRP cc_start: 0.8638 (m-10) cc_final: 0.8378 (m-10) outliers start: 40 outliers final: 29 residues processed: 96 average time/residue: 0.1548 time to fit residues: 23.8282 Evaluate side-chains 96 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10103 Z= 0.215 Angle : 0.567 9.587 13719 Z= 0.296 Chirality : 0.046 0.235 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.725 21.525 1390 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.28 % Allowed : 12.95 % Favored : 83.77 % 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: -1.63 (0.24), residues: 1238 helix: -0.70 (0.75), residues: 49 sheet: -0.84 (0.22), residues: 547 loop : -1.26 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.002 0.001 HIS B 603 PHE 0.021 0.001 PHE A 311 TYR 0.022 0.001 TYR A 269 ARG 0.006 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 73 time to evaluate : 1.123 Fit side-chains REVERT: A 219 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: A 311 PHE cc_start: 0.8231 (t80) cc_final: 0.7914 (t80) REVERT: B 508 TRP cc_start: 0.7381 (m100) cc_final: 0.6630 (m100) REVERT: B 524 ASN cc_start: 0.8744 (t0) cc_final: 0.8436 (t0) REVERT: B 597 TRP cc_start: 0.8647 (p-90) cc_final: 0.7648 (p-90) REVERT: B 616 TRP cc_start: 0.8639 (m-10) cc_final: 0.8266 (m-10) outliers start: 35 outliers final: 26 residues processed: 97 average time/residue: 0.1708 time to fit residues: 26.2408 Evaluate side-chains 97 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.219 Angle : 0.570 9.866 13719 Z= 0.297 Chirality : 0.046 0.237 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.697 21.862 1390 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.00 % Allowed : 13.32 % Favored : 83.68 % 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: -1.62 (0.24), residues: 1238 helix: -1.15 (0.70), residues: 55 sheet: -0.79 (0.23), residues: 541 loop : -1.25 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 590 HIS 0.003 0.001 HIS B 603 PHE 0.020 0.001 PHE A 311 TYR 0.021 0.001 TYR A 269 ARG 0.006 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 1.154 Fit side-chains REVERT: A 219 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: A 311 PHE cc_start: 0.8231 (t80) cc_final: 0.7912 (t80) REVERT: A 560 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7950 (tp-100) REVERT: B 524 ASN cc_start: 0.8744 (t0) cc_final: 0.8440 (t0) REVERT: B 597 TRP cc_start: 0.8652 (p-90) cc_final: 0.7685 (p-90) REVERT: B 616 TRP cc_start: 0.8630 (m-10) cc_final: 0.8372 (m-10) outliers start: 32 outliers final: 28 residues processed: 97 average time/residue: 0.1668 time to fit residues: 25.9662 Evaluate side-chains 99 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10103 Z= 0.268 Angle : 0.584 10.210 13719 Z= 0.304 Chirality : 0.047 0.238 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.773 23.185 1390 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.10 % Allowed : 13.23 % Favored : 83.68 % 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: -1.68 (0.24), residues: 1238 helix: -1.19 (0.70), residues: 55 sheet: -0.87 (0.23), residues: 541 loop : -1.25 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 508 HIS 0.002 0.001 HIS B 603 PHE 0.020 0.001 PHE A 311 TYR 0.022 0.001 TYR A 269 ARG 0.006 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 67 time to evaluate : 0.907 Fit side-chains REVERT: A 219 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: A 560 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7956 (tp-100) REVERT: B 524 ASN cc_start: 0.8788 (t0) cc_final: 0.8462 (t0) REVERT: B 597 TRP cc_start: 0.8638 (p-90) cc_final: 0.7632 (p-90) REVERT: B 616 TRP cc_start: 0.8627 (m-10) cc_final: 0.8334 (m-10) outliers start: 33 outliers final: 27 residues processed: 89 average time/residue: 0.1649 time to fit residues: 23.5621 Evaluate side-chains 96 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3743 r_free = 0.3743 target = 0.126523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089039 restraints weight = 14449.097| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.01 r_work: 0.3153 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10103 Z= 0.241 Angle : 0.581 10.242 13719 Z= 0.301 Chirality : 0.047 0.241 1489 Planarity : 0.003 0.036 1796 Dihedral : 4.738 22.839 1390 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.00 % Allowed : 13.32 % Favored : 83.68 % 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 (0.24), residues: 1238 helix: -1.16 (0.70), residues: 55 sheet: -0.87 (0.23), residues: 541 loop : -1.25 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 508 HIS 0.002 0.001 HIS B 603 PHE 0.022 0.001 PHE A 311 TYR 0.022 0.001 TYR A 269 ARG 0.006 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.36 seconds wall clock time: 40 minutes 26.67 seconds (2426.67 seconds total)