Starting phenix.real_space_refine on Wed Mar 4 03:47:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udc_26456/03_2026/7udc_26456.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5307 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4030 2.51 5 N 1092 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6425 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4331 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 27, 'TRANS': 514} Chain breaks: 3 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1716 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Time building chain proxies: 1.68, per 1000 atoms: 0.26 Number of scatterers: 6425 At special positions: 0 Unit cell: (92.88, 109.08, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1268 8.00 N 1092 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS C 36 " 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 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 231.5 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.631A pdb=" N CYS A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.942A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.347A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.745A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 removed outlier: 3.581A pdb=" N THR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.816A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 313 removed outlier: 4.065A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLN A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 359 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 361 through 375 removed outlier: 3.893A pdb=" N ASP A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Proline residue: A 392 - end of helix removed outlier: 3.529A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.741A pdb=" N TYR A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.304A pdb=" N ILE A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.848A pdb=" N ASP A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.958A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.708A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 28 through 64 Processing helix chain 'B' and resid 68 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.132A pdb=" N ASN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 149 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 204 through 221 removed outlier: 3.849A pdb=" N GLU B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 231 removed outlier: 3.756A pdb=" N ASP B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 73 removed outlier: 4.112A pdb=" N GLU C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 removed outlier: 4.021A pdb=" N PHE C 77 " --> pdb=" O ALA C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.050A pdb=" N LYS A 29 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 57 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 76 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 32 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 73 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 105 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR A 75 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 102 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A 129 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.659A pdb=" N TYR A 145 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 537 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY A 568 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 539 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 229 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266 353 hydrogen bonds defined for protein. 1050 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: 0.72 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2154 1.34 - 1.46: 1282 1.46 - 1.58: 3018 1.58 - 1.70: 1 1.70 - 1.82: 61 Bond restraints: 6516 Sorted by residual: bond pdb=" CB PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.32e+00 bond pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.11e-01 bond pdb=" CB ASP C 65 " pdb=" CG ASP C 65 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.54e-01 bond pdb=" CA THR B 23 " pdb=" CB THR B 23 " ideal model delta sigma weight residual 1.529 1.540 -0.011 1.62e-02 3.81e+03 4.97e-01 bond pdb=" CA THR B 161 " pdb=" CB THR B 161 " ideal model delta sigma weight residual 1.540 1.521 0.019 2.70e-02 1.37e+03 4.82e-01 ... (remaining 6511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 8626 1.75 - 3.50: 122 3.50 - 5.26: 25 5.26 - 7.01: 2 7.01 - 8.76: 1 Bond angle restraints: 8776 Sorted by residual: angle pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" CD PRO A 223 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" CB MET A 374 " pdb=" CG MET A 374 " pdb=" SD MET A 374 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" N GLU B 73 " pdb=" CA GLU B 73 " pdb=" CB GLU B 73 " ideal model delta sigma weight residual 110.28 114.20 -3.92 1.55e+00 4.16e-01 6.39e+00 angle pdb=" C ARG A 275 " pdb=" N VAL A 276 " pdb=" CA VAL A 276 " ideal model delta sigma weight residual 121.97 126.52 -4.55 1.80e+00 3.09e-01 6.38e+00 angle pdb=" N PRO A 223 " pdb=" CD PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 103.20 99.51 3.69 1.50e+00 4.44e-01 6.04e+00 ... (remaining 8771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3646 17.89 - 35.78: 349 35.78 - 53.66: 67 53.66 - 71.55: 18 71.55 - 89.44: 5 Dihedral angle restraints: 4085 sinusoidal: 1702 harmonic: 2383 Sorted by residual: dihedral pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " pdb=" CD GLU A 66 " pdb=" OE1 GLU A 66 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN B 50 " pdb=" CB ASN B 50 " pdb=" CG ASN B 50 " pdb=" OD1 ASN B 50 " ideal model delta sinusoidal sigma weight residual -90.00 -153.56 63.56 2 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " pdb=" OD1 ASP B 27 " ideal model delta sinusoidal sigma weight residual -30.00 -83.15 53.15 1 2.00e+01 2.50e-03 9.61e+00 ... (remaining 4082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 678 0.032 - 0.064: 225 0.064 - 0.096: 76 0.096 - 0.127: 22 0.127 - 0.159: 5 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" C PRO A 223 " pdb=" CB PRO A 223 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA GLU B 73 " pdb=" N GLU B 73 " pdb=" C GLU B 73 " pdb=" CB GLU B 73 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1003 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " -0.065 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO A 223 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 369 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU A 369 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU A 369 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 78 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 79 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.022 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 512 2.74 - 3.28: 6563 3.28 - 3.82: 10244 3.82 - 4.36: 11465 4.36 - 4.90: 20211 Nonbonded interactions: 48995 Sorted by model distance: nonbonded pdb=" NZ LYS A 29 " pdb=" OE1 GLU A 72 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A 75 " pdb=" OD2 ASP A 90 " model vdw 2.285 3.040 nonbonded pdb=" O GLN A 175 " pdb=" OG1 THR A 178 " model vdw 2.286 3.040 nonbonded pdb=" NH1 ARG A 464 " pdb=" OD2 ASP A 484 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASN A 442 " pdb=" ND2 ASN A 586 " model vdw 2.316 3.120 ... (remaining 48990 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 group one per residue 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.003 0.126 6517 Z= 0.130 Angle : 0.539 8.760 8778 Z= 0.296 Chirality : 0.038 0.159 1006 Planarity : 0.004 0.096 1129 Dihedral : 14.902 89.440 2522 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.31), residues: 788 helix: 2.44 (0.25), residues: 447 sheet: 0.47 (0.78), residues: 54 loop : -0.74 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.013 0.001 TYR A 531 PHE 0.017 0.001 PHE B 33 TRP 0.003 0.001 TRP A 563 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6516) covalent geometry : angle 0.53900 ( 8776) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.19078 ( 2) hydrogen bonds : bond 0.15273 ( 353) hydrogen bonds : angle 5.08423 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.8709 (tpp) cc_final: 0.8467 (tpp) REVERT: B 45 ASP cc_start: 0.8487 (t0) cc_final: 0.7606 (t0) REVERT: B 98 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 141 TYR cc_start: 0.9249 (t80) cc_final: 0.9010 (t80) REVERT: C 62 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8242 (tm-30) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.0701 time to fit residues: 13.5181 Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119936 restraints weight = 8366.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118437 restraints weight = 5465.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119830 restraints weight = 5674.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120628 restraints weight = 4395.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121422 restraints weight = 4160.026| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6517 Z= 0.125 Angle : 0.504 7.493 8778 Z= 0.267 Chirality : 0.040 0.144 1006 Planarity : 0.004 0.044 1129 Dihedral : 3.514 13.311 864 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.67 % Allowed : 8.06 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.30), residues: 788 helix: 2.54 (0.24), residues: 453 sheet: 0.58 (0.75), residues: 55 loop : -0.77 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.019 0.001 TYR B 243 PHE 0.011 0.001 PHE B 127 TRP 0.003 0.001 TRP A 288 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6516) covalent geometry : angle 0.50358 ( 8776) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.09380 ( 2) hydrogen bonds : bond 0.04393 ( 353) hydrogen bonds : angle 3.92226 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7852 (tmm-80) REVERT: A 387 MET cc_start: 0.8755 (mmm) cc_final: 0.8412 (mmm) REVERT: A 428 GLN cc_start: 0.8780 (tp40) cc_final: 0.8380 (tp-100) REVERT: B 30 MET cc_start: 0.7127 (tpp) cc_final: 0.6797 (tpp) REVERT: B 45 ASP cc_start: 0.8199 (t0) cc_final: 0.7343 (t0) REVERT: B 77 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 141 TYR cc_start: 0.9175 (t80) cc_final: 0.8639 (t80) REVERT: C 62 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8492 (tm-30) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.0760 time to fit residues: 12.7541 Evaluate side-chains 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116312 restraints weight = 8296.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114529 restraints weight = 5343.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116414 restraints weight = 5245.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117041 restraints weight = 4123.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117477 restraints weight = 4067.735| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6517 Z= 0.120 Angle : 0.476 5.632 8778 Z= 0.250 Chirality : 0.038 0.143 1006 Planarity : 0.004 0.041 1129 Dihedral : 3.460 12.998 864 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.39 % Allowed : 11.25 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.30), residues: 788 helix: 2.66 (0.24), residues: 453 sheet: 0.63 (0.74), residues: 55 loop : -0.77 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 28 TYR 0.021 0.001 TYR B 243 PHE 0.007 0.001 PHE B 127 TRP 0.004 0.001 TRP A 288 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6516) covalent geometry : angle 0.47572 ( 8776) SS BOND : bond 0.00101 ( 1) SS BOND : angle 1.06582 ( 2) hydrogen bonds : bond 0.04085 ( 353) hydrogen bonds : angle 3.75679 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8776 (mmm) cc_final: 0.8520 (mmm) REVERT: A 252 MET cc_start: 0.8601 (ttp) cc_final: 0.8305 (ttt) REVERT: A 305 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7888 (tmm-80) REVERT: A 387 MET cc_start: 0.8674 (mmm) cc_final: 0.8342 (mmm) REVERT: A 407 ILE cc_start: 0.9359 (tt) cc_final: 0.9113 (mt) REVERT: A 428 GLN cc_start: 0.8877 (tp40) cc_final: 0.8508 (tp-100) REVERT: A 550 MET cc_start: 0.8967 (ttm) cc_final: 0.8736 (ttm) REVERT: B 28 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6976 (mmm160) REVERT: B 30 MET cc_start: 0.7145 (tpp) cc_final: 0.6842 (tpp) REVERT: B 45 ASP cc_start: 0.8335 (t0) cc_final: 0.7446 (t0) REVERT: B 77 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 98 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 141 TYR cc_start: 0.9230 (t80) cc_final: 0.8710 (t80) REVERT: B 217 MET cc_start: 0.9095 (mmm) cc_final: 0.8722 (mmm) REVERT: C 62 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.0771 time to fit residues: 12.5057 Evaluate side-chains 112 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121327 restraints weight = 8434.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120584 restraints weight = 5302.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122817 restraints weight = 5222.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123337 restraints weight = 4001.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124046 restraints weight = 3672.053| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6517 Z= 0.109 Angle : 0.471 7.475 8778 Z= 0.249 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.392 12.393 864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.67 % Allowed : 12.92 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.31), residues: 788 helix: 2.71 (0.24), residues: 454 sheet: 0.59 (0.74), residues: 55 loop : -0.79 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.022 0.001 TYR B 243 PHE 0.013 0.001 PHE B 127 TRP 0.003 0.001 TRP A 288 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6516) covalent geometry : angle 0.47118 ( 8776) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.07863 ( 2) hydrogen bonds : bond 0.03828 ( 353) hydrogen bonds : angle 3.64309 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8798 (mmm) cc_final: 0.8522 (mmm) REVERT: A 163 GLN cc_start: 0.7973 (mm110) cc_final: 0.7752 (mp10) REVERT: A 276 VAL cc_start: 0.9283 (m) cc_final: 0.8812 (p) REVERT: A 305 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7910 (tmm-80) REVERT: A 374 MET cc_start: 0.8942 (mmm) cc_final: 0.8696 (mmm) REVERT: A 387 MET cc_start: 0.8711 (mmm) cc_final: 0.8379 (mmm) REVERT: A 429 HIS cc_start: 0.8500 (t-170) cc_final: 0.8115 (t70) REVERT: A 579 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 30 MET cc_start: 0.7190 (tpp) cc_final: 0.6962 (tpp) REVERT: B 45 ASP cc_start: 0.8248 (t0) cc_final: 0.7375 (t0) REVERT: B 77 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 98 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 131 MET cc_start: 0.8903 (tpp) cc_final: 0.8400 (mmm) REVERT: C 62 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 76 GLN cc_start: 0.8671 (tt0) cc_final: 0.8384 (mt0) outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 0.0795 time to fit residues: 12.9411 Evaluate side-chains 117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 10 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119042 restraints weight = 8454.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117671 restraints weight = 5499.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119666 restraints weight = 5428.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120314 restraints weight = 4215.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121417 restraints weight = 3887.734| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6517 Z= 0.108 Angle : 0.470 6.071 8778 Z= 0.245 Chirality : 0.038 0.143 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.361 12.704 864 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.67 % Allowed : 12.36 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.31), residues: 788 helix: 2.75 (0.24), residues: 455 sheet: 0.46 (0.75), residues: 54 loop : -0.74 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 28 TYR 0.024 0.001 TYR B 243 PHE 0.009 0.001 PHE B 127 TRP 0.003 0.001 TRP A 563 HIS 0.005 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6516) covalent geometry : angle 0.47021 ( 8776) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.12060 ( 2) hydrogen bonds : bond 0.03718 ( 353) hydrogen bonds : angle 3.55572 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.267 Fit side-chains REVERT: A 15 MET cc_start: 0.8814 (mmm) cc_final: 0.8545 (mmm) REVERT: A 163 GLN cc_start: 0.8040 (mm110) cc_final: 0.7788 (mp10) REVERT: A 276 VAL cc_start: 0.9288 (m) cc_final: 0.8818 (p) REVERT: A 305 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7927 (tmm-80) REVERT: A 374 MET cc_start: 0.8989 (mmm) cc_final: 0.8741 (mmm) REVERT: A 387 MET cc_start: 0.8712 (mmm) cc_final: 0.8337 (mmm) REVERT: A 429 HIS cc_start: 0.8399 (t-170) cc_final: 0.8029 (t70) REVERT: A 550 MET cc_start: 0.8727 (ttm) cc_final: 0.8438 (mtp) REVERT: B 45 ASP cc_start: 0.8295 (t0) cc_final: 0.7418 (t0) REVERT: B 77 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 98 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 141 TYR cc_start: 0.9295 (t80) cc_final: 0.8856 (t80) REVERT: C 62 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8476 (tm-30) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.0766 time to fit residues: 12.4154 Evaluate side-chains 115 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN B 207 ASN ** B 236 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 = 0.3804 r_free = 0.3804 target = 0.157528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117644 restraints weight = 8421.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116215 restraints weight = 5514.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118391 restraints weight = 5459.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118971 restraints weight = 4071.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119373 restraints weight = 4096.183| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6517 Z= 0.125 Angle : 0.479 7.425 8778 Z= 0.250 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.372 13.989 864 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 12.36 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.30), residues: 788 helix: 2.78 (0.24), residues: 455 sheet: 0.43 (0.75), residues: 54 loop : -0.72 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 28 TYR 0.024 0.001 TYR B 243 PHE 0.019 0.001 PHE B 127 TRP 0.004 0.001 TRP A 563 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6516) covalent geometry : angle 0.47882 ( 8776) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.18712 ( 2) hydrogen bonds : bond 0.03798 ( 353) hydrogen bonds : angle 3.55016 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.213 Fit side-chains REVERT: A 15 MET cc_start: 0.8826 (mmm) cc_final: 0.8529 (mmm) REVERT: A 163 GLN cc_start: 0.8105 (mm110) cc_final: 0.7830 (mp10) REVERT: A 276 VAL cc_start: 0.9277 (m) cc_final: 0.8817 (p) REVERT: A 305 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7961 (tmm-80) REVERT: A 374 MET cc_start: 0.9003 (mmm) cc_final: 0.8765 (mmm) REVERT: A 387 MET cc_start: 0.8667 (mmm) cc_final: 0.8291 (mmm) REVERT: A 429 HIS cc_start: 0.8433 (t-170) cc_final: 0.8065 (t70) REVERT: A 550 MET cc_start: 0.8776 (ttm) cc_final: 0.8491 (mtp) REVERT: B 77 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 62 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8477 (tm-30) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.0685 time to fit residues: 11.4581 Evaluate side-chains 120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117726 restraints weight = 8353.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116551 restraints weight = 5433.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118515 restraints weight = 5346.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119299 restraints weight = 4053.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120195 restraints weight = 3763.176| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6517 Z= 0.118 Angle : 0.485 6.578 8778 Z= 0.255 Chirality : 0.038 0.148 1006 Planarity : 0.004 0.039 1129 Dihedral : 3.373 13.955 864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.53 % Allowed : 13.47 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 788 helix: 2.75 (0.24), residues: 455 sheet: 0.47 (0.75), residues: 54 loop : -0.77 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.027 0.001 TYR B 141 PHE 0.031 0.001 PHE B 127 TRP 0.004 0.001 TRP A 563 HIS 0.005 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6516) covalent geometry : angle 0.48414 ( 8776) SS BOND : bond 0.00180 ( 1) SS BOND : angle 1.59905 ( 2) hydrogen bonds : bond 0.03834 ( 353) hydrogen bonds : angle 3.55683 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.258 Fit side-chains REVERT: A 15 MET cc_start: 0.8824 (mmm) cc_final: 0.8529 (mmm) REVERT: A 163 GLN cc_start: 0.8114 (mm110) cc_final: 0.7829 (mp10) REVERT: A 238 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 276 VAL cc_start: 0.9285 (m) cc_final: 0.8818 (p) REVERT: A 305 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7971 (tmm-80) REVERT: A 374 MET cc_start: 0.8992 (mmm) cc_final: 0.8758 (mmm) REVERT: A 387 MET cc_start: 0.8649 (mmm) cc_final: 0.8256 (mmm) REVERT: A 429 HIS cc_start: 0.8430 (t-170) cc_final: 0.8047 (t70) REVERT: A 550 MET cc_start: 0.8799 (ttm) cc_final: 0.8474 (mtp) REVERT: B 77 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 217 MET cc_start: 0.9009 (mmm) cc_final: 0.8671 (mmm) REVERT: C 62 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8465 (tm-30) outliers start: 11 outliers final: 9 residues processed: 117 average time/residue: 0.0676 time to fit residues: 11.2306 Evaluate side-chains 117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120489 restraints weight = 8304.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119663 restraints weight = 5228.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121124 restraints weight = 5273.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122115 restraints weight = 4092.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122331 restraints weight = 3885.019| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6517 Z= 0.120 Angle : 0.492 7.894 8778 Z= 0.255 Chirality : 0.038 0.141 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.380 13.805 864 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 14.44 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.30), residues: 788 helix: 2.68 (0.24), residues: 455 sheet: 0.47 (0.75), residues: 54 loop : -0.77 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 28 TYR 0.026 0.001 TYR B 243 PHE 0.016 0.001 PHE B 127 TRP 0.004 0.001 TRP A 563 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6516) covalent geometry : angle 0.49104 ( 8776) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.62745 ( 2) hydrogen bonds : bond 0.03807 ( 353) hydrogen bonds : angle 3.56459 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.255 Fit side-chains REVERT: A 15 MET cc_start: 0.8840 (mmm) cc_final: 0.8544 (mmm) REVERT: A 163 GLN cc_start: 0.8159 (mm110) cc_final: 0.7865 (mp10) REVERT: A 238 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8268 (t0) REVERT: A 275 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.8170 (tpp-160) REVERT: A 276 VAL cc_start: 0.9272 (m) cc_final: 0.8810 (p) REVERT: A 305 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7978 (tmm-80) REVERT: A 374 MET cc_start: 0.9002 (mmm) cc_final: 0.8777 (mmm) REVERT: A 387 MET cc_start: 0.8625 (mmm) cc_final: 0.8233 (mmm) REVERT: A 429 HIS cc_start: 0.8390 (t-170) cc_final: 0.7978 (t70) REVERT: A 550 MET cc_start: 0.8789 (ttm) cc_final: 0.8460 (mtp) REVERT: B 77 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 148 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7652 (ptm160) REVERT: B 217 MET cc_start: 0.9002 (mmm) cc_final: 0.8635 (mmm) REVERT: C 62 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 10 outliers final: 9 residues processed: 118 average time/residue: 0.0780 time to fit residues: 12.6063 Evaluate side-chains 120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117197 restraints weight = 8495.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115716 restraints weight = 5514.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117782 restraints weight = 5475.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118399 restraints weight = 4144.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118857 restraints weight = 4102.508| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6517 Z= 0.126 Angle : 0.486 7.790 8778 Z= 0.255 Chirality : 0.038 0.140 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.375 14.344 864 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.81 % Allowed : 14.03 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.30), residues: 788 helix: 2.71 (0.24), residues: 455 sheet: 0.45 (0.74), residues: 54 loop : -0.67 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 142 TYR 0.029 0.001 TYR B 141 PHE 0.009 0.001 PHE B 127 TRP 0.004 0.001 TRP A 563 HIS 0.006 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6516) covalent geometry : angle 0.48605 ( 8776) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.09189 ( 2) hydrogen bonds : bond 0.03831 ( 353) hydrogen bonds : angle 3.58674 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.255 Fit side-chains REVERT: A 15 MET cc_start: 0.8868 (mmm) cc_final: 0.8568 (mmm) REVERT: A 163 GLN cc_start: 0.8143 (mm110) cc_final: 0.7853 (mp10) REVERT: A 238 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8256 (t0) REVERT: A 275 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.8155 (tpp-160) REVERT: A 276 VAL cc_start: 0.9267 (m) cc_final: 0.8793 (p) REVERT: A 374 MET cc_start: 0.8995 (mmm) cc_final: 0.8777 (mmm) REVERT: A 387 MET cc_start: 0.8654 (mmm) cc_final: 0.8257 (mmm) REVERT: B 6 GLN cc_start: 0.8780 (tp40) cc_final: 0.8495 (tp40) REVERT: B 77 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 131 MET cc_start: 0.8988 (mmm) cc_final: 0.8258 (mpp) REVERT: B 217 MET cc_start: 0.9073 (mmm) cc_final: 0.8683 (mmm) REVERT: C 62 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8461 (tm-30) outliers start: 13 outliers final: 10 residues processed: 118 average time/residue: 0.0605 time to fit residues: 10.1327 Evaluate side-chains 118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.0030 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118786 restraints weight = 8315.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117630 restraints weight = 5485.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120014 restraints weight = 5459.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120249 restraints weight = 4194.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121120 restraints weight = 3800.733| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6517 Z= 0.107 Angle : 0.482 8.129 8778 Z= 0.250 Chirality : 0.038 0.141 1006 Planarity : 0.004 0.039 1129 Dihedral : 3.329 12.950 864 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.67 % Allowed : 14.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.31), residues: 788 helix: 2.66 (0.24), residues: 455 sheet: 0.59 (0.75), residues: 54 loop : -0.63 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.027 0.001 TYR B 243 PHE 0.010 0.001 PHE B 127 TRP 0.004 0.001 TRP A 563 HIS 0.006 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6516) covalent geometry : angle 0.48159 ( 8776) SS BOND : bond 0.00014 ( 1) SS BOND : angle 1.22648 ( 2) hydrogen bonds : bond 0.03658 ( 353) hydrogen bonds : angle 3.54774 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.180 Fit side-chains REVERT: A 15 MET cc_start: 0.8842 (mmm) cc_final: 0.8551 (mmm) REVERT: A 163 GLN cc_start: 0.8126 (mm110) cc_final: 0.7821 (mp10) REVERT: A 238 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (t0) REVERT: A 275 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8141 (tpp-160) REVERT: A 276 VAL cc_start: 0.9256 (m) cc_final: 0.8779 (p) REVERT: A 374 MET cc_start: 0.8983 (mmm) cc_final: 0.8765 (mmm) REVERT: A 387 MET cc_start: 0.8663 (mmm) cc_final: 0.8426 (mmm) REVERT: B 6 GLN cc_start: 0.8760 (tp40) cc_final: 0.8485 (tp40) REVERT: B 77 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 131 MET cc_start: 0.8965 (mmm) cc_final: 0.8357 (mpp) REVERT: C 62 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 65 ASP cc_start: 0.8574 (t0) cc_final: 0.8333 (t0) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.0682 time to fit residues: 10.9734 Evaluate side-chains 115 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117895 restraints weight = 8446.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116487 restraints weight = 5582.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118561 restraints weight = 5533.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119183 restraints weight = 4171.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119442 restraints weight = 4207.008| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6517 Z= 0.123 Angle : 0.482 7.684 8778 Z= 0.252 Chirality : 0.038 0.140 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.322 14.467 864 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.25 % Allowed : 14.86 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.30), residues: 788 helix: 2.63 (0.24), residues: 455 sheet: 0.57 (0.75), residues: 54 loop : -0.66 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.027 0.001 TYR B 243 PHE 0.009 0.001 PHE B 34 TRP 0.004 0.001 TRP A 563 HIS 0.005 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6516) covalent geometry : angle 0.48209 ( 8776) SS BOND : bond 0.00021 ( 1) SS BOND : angle 1.22129 ( 2) hydrogen bonds : bond 0.03782 ( 353) hydrogen bonds : angle 3.56903 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1086.51 seconds wall clock time: 19 minutes 24.74 seconds (1164.74 seconds total)