Starting phenix.real_space_refine on Tue Feb 11 13:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.map" model { file = "/net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snc_40622/02_2025/8snc_40622.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 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 Mn 2 7.51 5 S 35 5.16 5 C 3834 2.51 5 N 968 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5927 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4029 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 2 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 895 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BDP': 1, 'NAG': 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 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MN': 2, 'Y01': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 4.31, per 1000 atoms: 0.73 Number of scatterers: 5927 At special positions: 0 Unit cell: (74.7, 78.02, 142.76, 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) Mn 2 24.99 S 35 16.00 O 1088 8.00 N 968 7.00 C 3834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " BDP D 2 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 46.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 50 through 74 removed outlier: 3.685A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.932A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.508A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.741A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.726A pdb=" N GLN A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 5.110A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 331 through 356 removed outlier: 4.846A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 391 removed outlier: 3.685A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.942A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 7.374A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 198 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 317 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 227 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 319 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY A 229 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE A 321 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N CYS A 231 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL A 323 " --> pdb=" O CYS A 231 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N ILE A 233 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TRP A 325 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.285A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.789A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.660A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.538A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.562A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 924 1.31 - 1.44: 1817 1.44 - 1.56: 3281 1.56 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 6075 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C1 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 8174 2.48 - 4.96: 65 4.96 - 7.44: 11 7.44 - 9.92: 1 9.92 - 12.40: 2 Bond angle restraints: 8253 Sorted by residual: angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 121.11 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CBB Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBI Y01 A 601 " ideal model delta sigma weight residual 119.27 111.12 8.15 3.00e+00 1.11e-01 7.39e+00 angle pdb=" CA ASN A 78 " pdb=" CB ASN A 78 " pdb=" CG ASN A 78 " ideal model delta sigma weight residual 112.60 115.06 -2.46 1.00e+00 1.00e+00 6.07e+00 angle pdb=" CAJ Y01 A 601 " pdb=" CAO Y01 A 601 " pdb=" CBB Y01 A 601 " ideal model delta sigma weight residual 115.08 108.31 6.77 3.00e+00 1.11e-01 5.09e+00 ... (remaining 8248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3043 16.94 - 33.88: 413 33.88 - 50.82: 109 50.82 - 67.76: 28 67.76 - 84.71: 7 Dihedral angle restraints: 3600 sinusoidal: 1471 harmonic: 2129 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 52.75 40.25 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA VAL B 12 " pdb=" C VAL B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE A 476 " pdb=" C PHE A 476 " pdb=" N LEU A 477 " pdb=" CA LEU A 477 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 867 0.096 - 0.191: 38 0.191 - 0.287: 1 0.287 - 0.383: 1 0.383 - 0.478: 1 Chirality restraints: 908 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CBH Y01 A 601 " pdb=" CAT Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBF Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.53 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.83 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 905 not shown) Planarity restraints: 1017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 271 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 116 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C LEU A 116 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A 116 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 117 " 0.008 2.00e-02 2.50e+03 ... (remaining 1014 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 172 2.70 - 3.25: 5759 3.25 - 3.80: 9587 3.80 - 4.35: 11902 4.35 - 4.90: 20905 Nonbonded interactions: 48325 Sorted by model distance: nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 602 " model vdw 2.156 2.320 nonbonded pdb=" O ASN A 235 " pdb=" OG SER A 241 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASP A 203 " pdb="MN MN A 603 " model vdw 2.215 2.320 nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 602 " model vdw 2.262 2.320 nonbonded pdb=" O TYR B 32 " pdb=" NH2 ARG B 71 " model vdw 2.265 3.120 ... (remaining 48320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.112 6075 Z= 0.281 Angle : 0.596 12.403 8253 Z= 0.296 Chirality : 0.047 0.478 908 Planarity : 0.003 0.052 1017 Dihedral : 16.852 84.706 2239 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.16 % Allowed : 24.48 % Favored : 75.36 % 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: -0.17 (0.30), residues: 716 helix: 1.26 (0.29), residues: 297 sheet: 0.21 (0.44), residues: 140 loop : -1.85 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 PHE 0.009 0.001 PHE B 47 TYR 0.011 0.001 TYR A 414 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.638 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.1741 time to fit residues: 11.2494 Evaluate side-chains 42 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 497 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 = 0.3916 r_free = 0.3916 target = 0.173770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126361 restraints weight = 6384.503| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.03 r_work: 0.3240 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6075 Z= 0.183 Angle : 0.479 6.144 8253 Z= 0.259 Chirality : 0.042 0.153 908 Planarity : 0.003 0.048 1017 Dihedral : 5.819 45.195 928 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.08 % Allowed : 21.92 % Favored : 76.00 % 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: -0.00 (0.31), residues: 716 helix: 1.29 (0.28), residues: 305 sheet: 0.34 (0.43), residues: 145 loop : -1.76 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 246 HIS 0.001 0.001 HIS A 552 PHE 0.008 0.001 PHE A 476 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.494 Fit side-chains REVERT: A 472 TRP cc_start: 0.7910 (t60) cc_final: 0.7676 (t60) REVERT: C 67 PHE cc_start: 0.6479 (m-10) cc_final: 0.6054 (m-10) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.1395 time to fit residues: 12.0285 Evaluate side-chains 47 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 497 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 = 0.3906 r_free = 0.3906 target = 0.170524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122542 restraints weight = 6391.126| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.07 r_work: 0.3276 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6075 Z= 0.154 Angle : 0.442 5.369 8253 Z= 0.238 Chirality : 0.041 0.141 908 Planarity : 0.003 0.044 1017 Dihedral : 5.144 44.976 928 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.72 % Allowed : 22.72 % Favored : 74.56 % 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: 0.24 (0.31), residues: 716 helix: 1.49 (0.29), residues: 306 sheet: 0.52 (0.44), residues: 145 loop : -1.68 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 246 HIS 0.002 0.001 HIS A 552 PHE 0.007 0.001 PHE A 476 TYR 0.011 0.001 TYR A 414 ARG 0.002 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.663 Fit side-chains REVERT: A 472 TRP cc_start: 0.7670 (t60) cc_final: 0.7458 (t60) REVERT: C 67 PHE cc_start: 0.6308 (m-10) cc_final: 0.5987 (m-10) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.1319 time to fit residues: 11.6889 Evaluate side-chains 49 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 497 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 = 0.3910 r_free = 0.3910 target = 0.170805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122645 restraints weight = 6545.714| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.07 r_work: 0.3282 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.154 Angle : 0.440 5.373 8253 Z= 0.236 Chirality : 0.041 0.139 908 Planarity : 0.003 0.044 1017 Dihedral : 5.056 45.282 928 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 23.04 % Favored : 74.40 % 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: 0.33 (0.31), residues: 716 helix: 1.60 (0.29), residues: 304 sheet: 0.31 (0.44), residues: 151 loop : -1.51 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 358 HIS 0.002 0.001 HIS A 360 PHE 0.018 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.601 Fit side-chains REVERT: A 472 TRP cc_start: 0.7730 (t60) cc_final: 0.7530 (t60) REVERT: C 67 PHE cc_start: 0.6330 (m-10) cc_final: 0.6043 (m-10) outliers start: 16 outliers final: 6 residues processed: 53 average time/residue: 0.1295 time to fit residues: 10.4033 Evaluate side-chains 44 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 497 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 = 0.3907 r_free = 0.3907 target = 0.170487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122283 restraints weight = 6374.802| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.06 r_work: 0.3280 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6075 Z= 0.174 Angle : 0.438 5.387 8253 Z= 0.237 Chirality : 0.041 0.138 908 Planarity : 0.003 0.045 1017 Dihedral : 4.997 45.519 928 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.88 % Allowed : 23.04 % Favored : 74.08 % 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: 0.33 (0.31), residues: 716 helix: 1.53 (0.29), residues: 306 sheet: 0.33 (0.44), residues: 151 loop : -1.46 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.002 0.001 HIS A 552 PHE 0.009 0.001 PHE A 476 TYR 0.012 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.594 Fit side-chains REVERT: A 472 TRP cc_start: 0.7676 (t60) cc_final: 0.7475 (t60) REVERT: C 67 PHE cc_start: 0.6324 (m-10) cc_final: 0.6051 (m-10) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 0.1395 time to fit residues: 11.7918 Evaluate side-chains 50 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 307 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117657 restraints weight = 6418.534| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.13 r_work: 0.3208 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6075 Z= 0.290 Angle : 0.502 5.832 8253 Z= 0.269 Chirality : 0.043 0.145 908 Planarity : 0.003 0.046 1017 Dihedral : 5.340 47.292 928 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.84 % Allowed : 21.76 % Favored : 74.40 % 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: 0.04 (0.31), residues: 716 helix: 1.22 (0.29), residues: 306 sheet: 0.20 (0.44), residues: 151 loop : -1.52 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 360 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.606 Fit side-chains REVERT: A 307 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7579 (m110) REVERT: A 472 TRP cc_start: 0.7828 (t60) cc_final: 0.7615 (t60) REVERT: C 67 PHE cc_start: 0.6572 (m-10) cc_final: 0.6254 (m-10) outliers start: 24 outliers final: 14 residues processed: 64 average time/residue: 0.1582 time to fit residues: 14.3722 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122376 restraints weight = 6357.452| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.07 r_work: 0.3223 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6075 Z= 0.227 Angle : 0.477 6.429 8253 Z= 0.256 Chirality : 0.042 0.149 908 Planarity : 0.003 0.045 1017 Dihedral : 5.228 46.057 928 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.56 % Allowed : 23.20 % Favored : 74.24 % 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: 0.06 (0.31), residues: 716 helix: 1.24 (0.29), residues: 306 sheet: 0.18 (0.44), residues: 151 loop : -1.50 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.005 0.002 HIS A 195 PHE 0.010 0.001 PHE A 369 TYR 0.013 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.614 Fit side-chains REVERT: A 472 TRP cc_start: 0.7856 (t60) cc_final: 0.7643 (t60) REVERT: C 67 PHE cc_start: 0.6606 (m-10) cc_final: 0.6299 (m-10) outliers start: 16 outliers final: 15 residues processed: 57 average time/residue: 0.1452 time to fit residues: 12.1364 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.171106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122392 restraints weight = 6378.187| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.12 r_work: 0.3274 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6075 Z= 0.143 Angle : 0.452 10.112 8253 Z= 0.240 Chirality : 0.040 0.135 908 Planarity : 0.003 0.044 1017 Dihedral : 4.964 44.390 928 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.40 % Allowed : 23.20 % Favored : 74.40 % 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: 0.35 (0.31), residues: 716 helix: 1.52 (0.29), residues: 310 sheet: 0.18 (0.44), residues: 152 loop : -1.34 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.006 0.001 HIS A 195 PHE 0.010 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.657 Fit side-chains REVERT: C 67 PHE cc_start: 0.6499 (m-10) cc_final: 0.6225 (m-10) outliers start: 15 outliers final: 10 residues processed: 53 average time/residue: 0.1492 time to fit residues: 11.6003 Evaluate side-chains 50 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122261 restraints weight = 6534.277| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.39 r_work: 0.3371 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6075 Z= 0.170 Angle : 0.454 9.044 8253 Z= 0.243 Chirality : 0.041 0.143 908 Planarity : 0.003 0.044 1017 Dihedral : 4.948 45.338 928 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.56 % Allowed : 22.56 % Favored : 74.88 % 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: 0.41 (0.31), residues: 716 helix: 1.54 (0.29), residues: 311 sheet: 0.22 (0.44), residues: 152 loop : -1.30 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.005 0.002 HIS A 195 PHE 0.008 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.631 Fit side-chains REVERT: C 67 PHE cc_start: 0.6315 (m-10) cc_final: 0.6044 (m-10) outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.1498 time to fit residues: 12.1149 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122132 restraints weight = 6516.016| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.40 r_work: 0.3373 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 6075 Z= 0.193 Angle : 0.933 59.200 8253 Z= 0.560 Chirality : 0.042 0.292 908 Planarity : 0.004 0.057 1017 Dihedral : 4.987 45.240 928 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.24 % Allowed : 22.88 % Favored : 74.88 % 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: 0.42 (0.31), residues: 716 helix: 1.58 (0.29), residues: 310 sheet: 0.23 (0.44), residues: 152 loop : -1.33 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.004 0.001 HIS A 195 PHE 0.007 0.001 PHE B 67 TYR 0.012 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.574 Fit side-chains REVERT: C 67 PHE cc_start: 0.6328 (m-10) cc_final: 0.6056 (m-10) outliers start: 14 outliers final: 13 residues processed: 54 average time/residue: 0.1470 time to fit residues: 11.4286 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.174022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122221 restraints weight = 6561.237| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.41 r_work: 0.3374 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6075 Z= 0.189 Angle : 0.812 46.978 8253 Z= 0.484 Chirality : 0.041 0.241 908 Planarity : 0.004 0.057 1017 Dihedral : 4.987 45.240 928 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.24 % Allowed : 22.88 % Favored : 74.88 % 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: 0.42 (0.31), residues: 716 helix: 1.58 (0.29), residues: 310 sheet: 0.23 (0.44), residues: 152 loop : -1.33 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.004 0.001 HIS A 195 PHE 0.007 0.001 PHE B 67 TYR 0.012 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.34 seconds wall clock time: 64 minutes 11.85 seconds (3851.85 seconds total)