Starting phenix.real_space_refine on Thu Jun 5 09:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snc_40622/06_2025/8snc_40622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snc_40622/06_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_40622/06_2025/8snc_40622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snc_40622/06_2025/8snc_40622.map" model { file = "/net/cci-nas-00/data/ceres_data/8snc_40622/06_2025/8snc_40622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snc_40622/06_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-5710/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: 4.30, 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: 1.66 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: 0.59 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: 1.95 Time building geometry restraints manager: 1.81 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: 0.710 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- 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 6077 Z= 0.230 Angle : 0.597 12.403 8258 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 Details of bonding type rmsd hydrogen bonds : bond 0.14436 ( 304) hydrogen bonds : angle 6.16027 ( 852) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.11703 ( 2) link_BETA1-3 : bond 0.00333 ( 1) link_BETA1-3 : angle 1.43960 ( 3) covalent geometry : bond 0.00470 ( 6075) covalent geometry : angle 0.59614 ( 8253) *********************** 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 : 0.692 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.2179 time to fit residues: 14.3715 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 : 0.609 ------------------------------------------------------------------------------- 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 = 0.173769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126381 restraints weight = 6384.481| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.04 r_work: 0.3241 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 6077 Z= 0.132 Angle : 0.482 6.144 8258 Z= 0.260 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 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 304) hydrogen bonds : angle 4.80992 ( 852) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.58294 ( 2) link_BETA1-3 : bond 0.00687 ( 1) link_BETA1-3 : angle 2.49268 ( 3) covalent geometry : bond 0.00286 ( 6075) covalent geometry : angle 0.47937 ( 8253) *********************** 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 : 0.624 Fit side-chains REVERT: A 472 TRP cc_start: 0.7916 (t60) cc_final: 0.7682 (t60) REVERT: C 67 PHE cc_start: 0.6478 (m-10) cc_final: 0.6052 (m-10) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.1534 time to fit residues: 13.1999 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 : 0.604 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.171566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123787 restraints weight = 6384.132| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.07 r_work: 0.3299 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6077 Z= 0.102 Angle : 0.436 5.355 8258 Z= 0.235 Chirality : 0.041 0.145 908 Planarity : 0.003 0.044 1017 Dihedral : 5.089 44.545 928 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 0.36 (0.31), residues: 716 helix: 1.60 (0.29), residues: 308 sheet: 0.53 (0.44), residues: 145 loop : -1.63 (0.36), residues: 263 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 0.007 0.001 PHE B 47 TYR 0.010 0.001 TYR A 414 ARG 0.002 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 304) hydrogen bonds : angle 4.40668 ( 852) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.19679 ( 2) link_BETA1-3 : bond 0.00416 ( 1) link_BETA1-3 : angle 2.04693 ( 3) covalent geometry : bond 0.00212 ( 6075) covalent geometry : angle 0.43451 ( 8253) *********************** 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 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.646 Fit side-chains REVERT: A 472 TRP cc_start: 0.7650 (t60) cc_final: 0.7442 (t60) REVERT: C 67 PHE cc_start: 0.6248 (m-10) cc_final: 0.5930 (m-10) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.1519 time to fit residues: 12.8727 Evaluate side-chains 48 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.172328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124290 restraints weight = 6523.483| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.08 r_work: 0.3301 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6077 Z= 0.099 Angle : 0.430 5.358 8258 Z= 0.231 Chirality : 0.040 0.137 908 Planarity : 0.003 0.044 1017 Dihedral : 4.988 44.888 928 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 23.52 % 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: 0.43 (0.31), residues: 716 helix: 1.71 (0.29), residues: 304 sheet: 0.34 (0.45), residues: 151 loop : -1.50 (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 552 PHE 0.016 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 304) hydrogen bonds : angle 4.24822 ( 852) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.10177 ( 2) link_BETA1-3 : bond 0.00411 ( 1) link_BETA1-3 : angle 2.04696 ( 3) covalent geometry : bond 0.00207 ( 6075) covalent geometry : angle 0.42830 ( 8253) *********************** 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 53 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.582 Fit side-chains REVERT: C 67 PHE cc_start: 0.6208 (m-10) cc_final: 0.5927 (m-10) outliers start: 14 outliers final: 6 residues processed: 52 average time/residue: 0.1260 time to fit residues: 10.1349 Evaluate side-chains 46 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 C residue 33 THR 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.169430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121154 restraints weight = 6408.394| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.08 r_work: 0.3214 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6077 Z= 0.191 Angle : 0.502 5.440 8258 Z= 0.270 Chirality : 0.043 0.138 908 Planarity : 0.004 0.046 1017 Dihedral : 5.355 47.555 928 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.36 % Allowed : 22.40 % 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: 0.07 (0.31), residues: 716 helix: 1.21 (0.29), residues: 306 sheet: 0.25 (0.44), residues: 151 loop : -1.49 (0.35), 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 360 PHE 0.014 0.001 PHE A 369 TYR 0.015 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 304) hydrogen bonds : angle 4.39297 ( 852) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.35337 ( 2) link_BETA1-3 : bond 0.00301 ( 1) link_BETA1-3 : angle 1.88169 ( 3) covalent geometry : bond 0.00449 ( 6075) covalent geometry : angle 0.50093 ( 8253) *********************** 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 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.623 Fit side-chains REVERT: A 140 ASP cc_start: 0.7838 (p0) cc_final: 0.7602 (p0) REVERT: A 307 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7601 (m-40) REVERT: C 67 PHE cc_start: 0.6561 (m-10) cc_final: 0.6234 (m-10) outliers start: 21 outliers final: 13 residues processed: 63 average time/residue: 0.1315 time to fit residues: 12.1454 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 : 0.540 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 MET 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 B residue 20 VAL 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: 0.9980 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.170467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122119 restraints weight = 6357.791| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.06 r_work: 0.3274 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6077 Z= 0.112 Angle : 0.441 5.373 8258 Z= 0.237 Chirality : 0.041 0.139 908 Planarity : 0.003 0.045 1017 Dihedral : 5.035 44.664 928 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 23.20 % Favored : 73.92 % 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: 0.28 (0.31), residues: 716 helix: 1.45 (0.29), residues: 307 sheet: 0.25 (0.44), residues: 151 loop : -1.40 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 PHE 0.008 0.001 PHE A 476 TYR 0.012 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 304) hydrogen bonds : angle 4.22301 ( 852) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.07231 ( 2) link_BETA1-3 : bond 0.00432 ( 1) link_BETA1-3 : angle 2.00025 ( 3) covalent geometry : bond 0.00250 ( 6075) covalent geometry : angle 0.43920 ( 8253) *********************** 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 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.616 Fit side-chains REVERT: A 307 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7360 (m-40) REVERT: C 67 PHE cc_start: 0.6425 (m-10) cc_final: 0.6138 (m-10) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 0.1415 time to fit residues: 11.5639 Evaluate side-chains 52 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 307 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.167745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118586 restraints weight = 6386.435| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.13 r_work: 0.3217 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6077 Z= 0.167 Angle : 0.490 8.944 8258 Z= 0.260 Chirality : 0.042 0.142 908 Planarity : 0.003 0.046 1017 Dihedral : 5.228 46.896 928 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.88 % Allowed : 22.88 % 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: 0.12 (0.31), residues: 716 helix: 1.25 (0.29), residues: 307 sheet: 0.18 (0.44), residues: 152 loop : -1.40 (0.36), residues: 257 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 0.012 0.001 PHE A 369 TYR 0.013 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 304) hydrogen bonds : angle 4.28917 ( 852) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.17890 ( 2) link_BETA1-3 : bond 0.00455 ( 1) link_BETA1-3 : angle 1.88709 ( 3) covalent geometry : bond 0.00395 ( 6075) covalent geometry : angle 0.48866 ( 8253) *********************** 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 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.606 Fit side-chains REVERT: A 140 ASP cc_start: 0.7962 (p0) cc_final: 0.7746 (p0) REVERT: A 307 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: C 67 PHE cc_start: 0.6571 (m-10) cc_final: 0.6262 (m-10) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 0.1694 time to fit residues: 13.4192 Evaluate side-chains 54 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 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 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 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: 2.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.171504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123560 restraints weight = 6380.351| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.07 r_work: 0.3245 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6077 Z= 0.131 Angle : 0.463 6.733 8258 Z= 0.247 Chirality : 0.041 0.133 908 Planarity : 0.003 0.045 1017 Dihedral : 5.115 45.571 928 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.24 % Allowed : 23.20 % 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: 1.34 (0.28), residues: 311 sheet: 0.15 (0.44), residues: 152 loop : -1.31 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 PHE 0.008 0.001 PHE A 385 TYR 0.013 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 304) hydrogen bonds : angle 4.23312 ( 852) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.16133 ( 2) link_BETA1-3 : bond 0.00492 ( 1) link_BETA1-3 : angle 1.92064 ( 3) covalent geometry : bond 0.00301 ( 6075) covalent geometry : angle 0.46133 ( 8253) *********************** 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 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.589 Fit side-chains REVERT: A 307 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7529 (m-40) REVERT: C 67 PHE cc_start: 0.6562 (m-10) cc_final: 0.6259 (m-10) outliers start: 14 outliers final: 10 residues processed: 52 average time/residue: 0.1506 time to fit residues: 11.4232 Evaluate side-chains 51 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 307 ASN 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 Chi-restraints excluded: chain C residue 97 LEU 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: 0.7980 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** 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 = 0.4093 r_free = 0.4093 target = 0.174321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122643 restraints weight = 6548.187| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.41 r_work: 0.3376 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6077 Z= 0.110 Angle : 0.448 7.560 8258 Z= 0.239 Chirality : 0.041 0.139 908 Planarity : 0.003 0.044 1017 Dihedral : 4.959 44.915 928 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.40 % Allowed : 23.04 % 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: 0.40 (0.31), residues: 716 helix: 1.52 (0.29), residues: 310 sheet: 0.23 (0.44), residues: 150 loop : -1.26 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 PHE 0.007 0.001 PHE A 385 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 304) hydrogen bonds : angle 4.15076 ( 852) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.10019 ( 2) link_BETA1-3 : bond 0.00466 ( 1) link_BETA1-3 : angle 1.89791 ( 3) covalent geometry : bond 0.00241 ( 6075) covalent geometry : angle 0.44675 ( 8253) *********************** 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 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.577 Fit side-chains REVERT: A 307 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: C 67 PHE cc_start: 0.6355 (m-10) cc_final: 0.6079 (m-10) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.1231 time to fit residues: 10.3471 Evaluate side-chains 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 307 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.174873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123170 restraints weight = 6505.207| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.40 r_work: 0.3382 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6077 Z= 0.106 Angle : 0.449 9.706 8258 Z= 0.238 Chirality : 0.040 0.135 908 Planarity : 0.003 0.044 1017 Dihedral : 4.879 44.828 928 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.40 % Allowed : 22.88 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 716 helix: 1.61 (0.29), residues: 310 sheet: 0.27 (0.44), residues: 150 loop : -1.24 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 358 HIS 0.004 0.002 HIS A 195 PHE 0.011 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 304) hydrogen bonds : angle 4.09609 ( 852) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.10227 ( 2) link_BETA1-3 : bond 0.00472 ( 1) link_BETA1-3 : angle 1.84022 ( 3) covalent geometry : bond 0.00233 ( 6075) covalent geometry : angle 0.44778 ( 8253) ********************** 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 62 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.668 Fit side-chains REVERT: A 307 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: C 67 PHE cc_start: 0.6304 (m-10) cc_final: 0.6031 (m-10) outliers start: 15 outliers final: 10 residues processed: 59 average time/residue: 0.1753 time to fit residues: 15.0678 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 307 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 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 2 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** 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 = 0.4095 r_free = 0.4095 target = 0.174579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122936 restraints weight = 6537.434| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.40 r_work: 0.3408 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6077 Z= 0.113 Angle : 0.458 11.032 8258 Z= 0.242 Chirality : 0.041 0.150 908 Planarity : 0.003 0.044 1017 Dihedral : 4.878 44.952 928 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.56 % Allowed : 22.72 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.31), residues: 716 helix: 1.61 (0.29), residues: 310 sheet: 0.30 (0.44), residues: 150 loop : -1.21 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 358 HIS 0.004 0.001 HIS A 195 PHE 0.007 0.001 PHE A 385 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 304) hydrogen bonds : angle 4.08537 ( 852) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.11332 ( 2) link_BETA1-3 : bond 0.00488 ( 1) link_BETA1-3 : angle 1.79927 ( 3) covalent geometry : bond 0.00252 ( 6075) covalent geometry : angle 0.45701 ( 8253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.33 seconds wall clock time: 68 minutes 3.15 seconds (4083.15 seconds total)