Starting phenix.real_space_refine on Thu Jul 2 01:59:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.map" model { file = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2026/8d48_27177.cif" } 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3498 2.51 5 N 926 2.21 5 O 1097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 2134 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 271, 2134 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2178 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "L" Number of atoms: 1711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1708 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 220, 1708 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1742 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.99, per 1000 atoms: 0.36 Number of scatterers: 5545 At special positions: 0 Unit cell: (77.5411, 115.886, 113.329, 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 24 16.00 O 1097 8.00 N 926 7.00 C 3498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 331 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 340.3 milliseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1330 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 6.9% alpha, 32.8% 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 338 through 343 removed outlier: 3.692A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.675A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.688A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.757A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.079A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.757A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.628A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.506A pdb=" N SER H 58 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 67 through 68 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.403A pdb=" N GLY H 141 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.403A pdb=" N GLY H 141 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 186 " --> pdb=" O VAL H 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 153 through 157 Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.096A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.641A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.727A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.942A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.083A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154 166 hydrogen bonds defined for protein. 402 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: 0.91 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1687 1.33 - 1.47: 1544 1.47 - 1.61: 2423 1.61 - 1.74: 1 1.74 - 1.88: 28 Bond restraints: 5683 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" CB PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.11e+01 bond pdb=" N VAL L 27B" pdb=" CA VAL L 27B" ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" CA SER L 27F" pdb=" CB SER L 27F" ideal model delta sigma weight residual 1.541 1.505 0.036 1.20e-02 6.94e+03 9.10e+00 bond pdb=" CA TYR A 351 " pdb=" C TYR A 351 " ideal model delta sigma weight residual 1.523 1.577 -0.053 1.80e-02 3.09e+03 8.81e+00 ... (remaining 5678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 7657 3.12 - 6.24: 73 6.24 - 9.35: 10 9.35 - 12.47: 0 12.47 - 15.59: 2 Bond angle restraints: 7742 Sorted by residual: angle pdb=" CA PRO H 214 " pdb=" N PRO H 214 " pdb=" CD PRO H 214 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 110.42 117.99 -7.57 9.60e-01 1.09e+00 6.22e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 128.65 -14.25 2.30e+00 1.89e-01 3.84e+01 angle pdb=" N ALA A 352 " pdb=" CA ALA A 352 " pdb=" CB ALA A 352 " ideal model delta sigma weight residual 111.65 120.29 -8.64 1.40e+00 5.10e-01 3.81e+01 angle pdb=" N PRO H 214 " pdb=" CD PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 103.20 96.03 7.17 1.50e+00 4.44e-01 2.28e+01 ... (remaining 7737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2971 17.87 - 35.75: 324 35.75 - 53.62: 81 53.62 - 71.50: 10 71.50 - 89.37: 4 Dihedral angle restraints: 3390 sinusoidal: 1306 harmonic: 2084 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 33.62 59.38 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -32.29 -53.71 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CA GLU H 150 " pdb=" C GLU H 150 " pdb=" N PRO H 151 " pdb=" CA PRO H 151 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 3387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 699 0.058 - 0.116: 141 0.116 - 0.173: 19 0.173 - 0.231: 3 0.231 - 0.289: 2 Chirality restraints: 864 Sorted by residual: chirality pdb=" CA ALA A 352 " pdb=" N ALA A 352 " pdb=" C ALA A 352 " pdb=" CB ALA A 352 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA VAL A 350 " pdb=" N VAL A 350 " pdb=" C VAL A 350 " pdb=" CB VAL A 350 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL H 223 " pdb=" N VAL H 223 " pdb=" C VAL H 223 " pdb=" CB VAL H 223 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 861 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 150 " -0.092 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO H 151 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 213 " -0.092 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO H 214 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO H 214 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO H 214 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 27A" 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN L 27A" -0.060 2.00e-02 2.50e+03 pdb=" O ASN L 27A" 0.023 2.00e-02 2.50e+03 pdb=" N VAL L 27B" 0.020 2.00e-02 2.50e+03 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 3 2.23 - 2.90: 2320 2.90 - 3.57: 7034 3.57 - 4.23: 11297 4.23 - 4.90: 19319 Nonbonded interactions: 39973 Sorted by model distance: nonbonded pdb=" NH2 ARG H 222 " pdb=" OE2 GLU H 226 " model vdw 1.565 3.120 nonbonded pdb=" OD1 ASP H 86 " pdb=" OH TYR H 90 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.219 3.120 nonbonded pdb=" OG SER H 156 " pdb=" OD1 ASN H 209 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 383 " pdb=" O THR A 385 " model vdw 2.247 3.040 ... (remaining 39968 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=0.00 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 0.166 5695 Z= 0.238 Angle : 0.818 15.589 7768 Z= 0.475 Chirality : 0.049 0.289 864 Planarity : 0.008 0.141 1002 Dihedral : 15.506 89.370 2030 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 19.74 % Favored : 80.26 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 7.32 % 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: -1.11 (0.31), residues: 713 helix: -3.19 (0.78), residues: 27 sheet: 0.49 (0.36), residues: 214 loop : -1.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.011 0.001 TYR L 49 PHE 0.015 0.001 PHE A 374 TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 ( 5683) covalent geometry : angle 0.80680 / 0.47 ( 7742) SS BOND : bond 0.00759 / 0.37 ( 10) SS BOND : angle 1.55202 / 0.89 ( 20) hydrogen bonds : bond 0.20058 / 13.13 ( 144) hydrogen bonds : angle 6.89286 / 4.90 ( 402) link_BETA1-4 : bond 0.00201 / 0.11 ( 1) link_BETA1-4 : angle 4.03111 / 2.13 ( 3) link_NAG-ASN : bond 0.00896 / 0.47 ( 1) link_NAG-ASN : angle 4.52327 / 2.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.226 Fit side-chains REVERT: A 409 GLN cc_start: 0.7561 (tp40) cc_final: 0.7253 (tp40) REVERT: L 81 GLU cc_start: 0.8154 (pp20) cc_final: 0.7945 (pp20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0874 time to fit residues: 9.6515 Evaluate side-chains 74 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 409 GLN A 437 ASN A 450 ASN H 172 HIS L 37 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140813 restraints weight = 22143.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141288 restraints weight = 23054.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141987 restraints weight = 15277.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142481 restraints weight = 12608.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142845 restraints weight = 10546.032| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5695 Z= 0.163 Angle : 0.725 14.036 7768 Z= 0.372 Chirality : 0.047 0.179 864 Planarity : 0.007 0.108 1002 Dihedral : 4.636 29.496 779 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.05 % Allowed : 19.74 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.01 (0.31), residues: 713 helix: -3.23 (0.86), residues: 21 sheet: 0.58 (0.35), residues: 218 loop : -1.23 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.024 0.002 TYR L 92 PHE 0.016 0.002 PHE A 456 TRP 0.020 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 5683) covalent geometry : angle 0.71391 / 0.37 ( 7742) SS BOND : bond 0.00886 / 0.46 ( 10) SS BOND : angle 1.69451 / 1.04 ( 20) hydrogen bonds : bond 0.04345 / 2.94 ( 144) hydrogen bonds : angle 6.01019 / 4.23 ( 402) link_BETA1-4 : bond 0.01507 / 0.79 ( 1) link_BETA1-4 : angle 3.57364 / 1.88 ( 3) link_NAG-ASN : bond 0.01501 / 0.79 ( 1) link_NAG-ASN : angle 3.94589 / 2.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: H 178 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8313 (tt) REVERT: L 81 GLU cc_start: 0.8253 (pp20) cc_final: 0.7984 (pp20) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.0926 time to fit residues: 10.6627 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain L residue 50 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN ** L 147 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122393 restraints weight = 27261.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123838 restraints weight = 26480.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124031 restraints weight = 10442.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124032 restraints weight = 7330.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124034 restraints weight = 7328.330| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5695 Z= 0.196 Angle : 0.758 14.283 7768 Z= 0.392 Chirality : 0.048 0.182 864 Planarity : 0.006 0.076 1002 Dihedral : 4.866 27.782 779 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.69 % Allowed : 19.26 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.18 (0.31), residues: 713 helix: -3.34 (0.83), residues: 21 sheet: 0.27 (0.34), residues: 238 loop : -1.30 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.022 0.002 TYR L 92 PHE 0.022 0.002 PHE A 562 TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 ( 5683) covalent geometry : angle 0.74676 / 0.39 ( 7742) SS BOND : bond 0.00936 / 0.49 ( 10) SS BOND : angle 1.84796 / 1.16 ( 20) hydrogen bonds : bond 0.04623 / 3.15 ( 144) hydrogen bonds : angle 6.04509 / 4.25 ( 402) link_BETA1-4 : bond 0.01371 / 0.72 ( 1) link_BETA1-4 : angle 3.27179 / 1.72 ( 3) link_NAG-ASN : bond 0.01359 / 0.72 ( 1) link_NAG-ASN : angle 4.05662 / 2.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.270 Fit side-chains REVERT: A 586 ASP cc_start: 0.7792 (t0) cc_final: 0.7560 (t0) REVERT: H 156 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7834 (m) REVERT: L 81 GLU cc_start: 0.8316 (pp20) cc_final: 0.7989 (pp20) outliers start: 23 outliers final: 17 residues processed: 94 average time/residue: 0.0997 time to fit residues: 11.8124 Evaluate side-chains 90 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 50 TRP Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 147 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.155667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121569 restraints weight = 23053.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121899 restraints weight = 24266.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122466 restraints weight = 8901.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122938 restraints weight = 8866.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123161 restraints weight = 9462.129| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5695 Z= 0.181 Angle : 0.734 14.131 7768 Z= 0.377 Chirality : 0.048 0.179 864 Planarity : 0.006 0.060 1002 Dihedral : 4.892 28.296 779 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.65 % Allowed : 19.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.17 (0.31), residues: 713 helix: -3.40 (0.83), residues: 21 sheet: 0.28 (0.34), residues: 235 loop : -1.28 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.018 0.002 TYR L 49 PHE 0.017 0.002 PHE A 562 TRP 0.020 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 5683) covalent geometry : angle 0.72296 / 0.37 ( 7742) SS BOND : bond 0.00910 / 0.47 ( 10) SS BOND : angle 1.80390 / 1.12 ( 20) hydrogen bonds : bond 0.04100 / 2.79 ( 144) hydrogen bonds : angle 5.98081 / 4.23 ( 402) link_BETA1-4 : bond 0.01516 / 0.80 ( 1) link_BETA1-4 : angle 3.10361 / 1.63 ( 3) link_NAG-ASN : bond 0.01294 / 0.68 ( 1) link_NAG-ASN : angle 4.04113 / 2.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.4787 (m-80) REVERT: L 81 GLU cc_start: 0.8323 (pp20) cc_final: 0.7994 (pp20) outliers start: 29 outliers final: 23 residues processed: 91 average time/residue: 0.0856 time to fit residues: 10.1730 Evaluate side-chains 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 50 TRP Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.156927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123738 restraints weight = 25556.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124668 restraints weight = 24515.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124934 restraints weight = 10752.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125438 restraints weight = 9708.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125515 restraints weight = 8823.945| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5695 Z= 0.141 Angle : 0.688 13.788 7768 Z= 0.351 Chirality : 0.046 0.172 864 Planarity : 0.005 0.051 1002 Dihedral : 4.666 26.941 779 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.69 % Allowed : 20.06 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.06 (0.31), residues: 713 helix: -3.39 (0.82), residues: 21 sheet: 0.36 (0.34), residues: 236 loop : -1.21 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.016 0.001 TYR L 91 PHE 0.013 0.001 PHE A 497 TRP 0.018 0.002 TRP A 436 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 5683) covalent geometry : angle 0.67645 / 0.35 ( 7742) SS BOND : bond 0.00825 / 0.42 ( 10) SS BOND : angle 1.66106 / 1.00 ( 20) hydrogen bonds : bond 0.03631 / 2.47 ( 144) hydrogen bonds : angle 5.81289 / 4.12 ( 402) link_BETA1-4 : bond 0.01398 / 0.74 ( 1) link_BETA1-4 : angle 3.05442 / 1.60 ( 3) link_NAG-ASN : bond 0.01238 / 0.65 ( 1) link_NAG-ASN : angle 4.17617 / 2.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5475 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: L 81 GLU cc_start: 0.8278 (pp20) cc_final: 0.7952 (pp20) outliers start: 23 outliers final: 22 residues processed: 86 average time/residue: 0.0848 time to fit residues: 9.4970 Evaluate side-chains 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 147 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.155547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133672 restraints weight = 16138.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133059 restraints weight = 21755.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131691 restraints weight = 7919.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131695 restraints weight = 5051.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131695 restraints weight = 5031.849| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5695 Z= 0.171 Angle : 0.710 13.976 7768 Z= 0.363 Chirality : 0.047 0.171 864 Planarity : 0.005 0.051 1002 Dihedral : 4.856 28.290 779 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.14 % Allowed : 18.94 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.08 (0.31), residues: 713 helix: -3.43 (0.82), residues: 21 sheet: 0.39 (0.34), residues: 238 loop : -1.25 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 71 TYR 0.019 0.002 TYR L 49 PHE 0.014 0.002 PHE A 562 TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 5683) covalent geometry : angle 0.69816 / 0.36 ( 7742) SS BOND : bond 0.00898 / 0.46 ( 10) SS BOND : angle 1.75404 / 1.08 ( 20) hydrogen bonds : bond 0.03883 / 2.64 ( 144) hydrogen bonds : angle 5.80995 / 4.12 ( 402) link_BETA1-4 : bond 0.01374 / 0.72 ( 1) link_BETA1-4 : angle 2.99089 / 1.57 ( 3) link_NAG-ASN : bond 0.01203 / 0.63 ( 1) link_NAG-ASN : angle 4.10164 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4401 (m-80) REVERT: L 81 GLU cc_start: 0.8215 (pp20) cc_final: 0.7894 (pp20) outliers start: 32 outliers final: 27 residues processed: 93 average time/residue: 0.0848 time to fit residues: 10.2683 Evaluate side-chains 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 50 TRP Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 70 optimal weight: 0.2980 chunk 6 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** L 147 GLN ** 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 = 0.3835 r_free = 0.3835 target = 0.159464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126136 restraints weight = 26341.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127621 restraints weight = 23602.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127401 restraints weight = 10417.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127781 restraints weight = 11156.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128117 restraints weight = 9148.309| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5695 Z= 0.119 Angle : 0.666 13.232 7768 Z= 0.340 Chirality : 0.045 0.170 864 Planarity : 0.005 0.047 1002 Dihedral : 4.440 26.302 779 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.41 % Allowed : 22.31 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.85 (0.31), residues: 713 helix: -3.30 (0.83), residues: 21 sheet: 0.68 (0.34), residues: 226 loop : -1.13 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.014 0.001 TYR L 91 PHE 0.009 0.001 PHE A 429 TRP 0.016 0.001 TRP A 436 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5683) covalent geometry : angle 0.65444 / 0.34 ( 7742) SS BOND : bond 0.00746 / 0.37 ( 10) SS BOND : angle 1.50224 / 0.87 ( 20) hydrogen bonds : bond 0.03101 / 2.10 ( 144) hydrogen bonds : angle 5.59894 / 3.99 ( 402) link_BETA1-4 : bond 0.01330 / 0.70 ( 1) link_BETA1-4 : angle 2.99421 / 1.57 ( 3) link_NAG-ASN : bond 0.01216 / 0.64 ( 1) link_NAG-ASN : angle 4.19407 / 2.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4612 (m-80) outliers start: 15 outliers final: 13 residues processed: 77 average time/residue: 0.0951 time to fit residues: 9.3048 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** L 147 GLN ** 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 = 0.3812 r_free = 0.3812 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123088 restraints weight = 15226.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124145 restraints weight = 21261.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124162 restraints weight = 10628.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124657 restraints weight = 9631.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124506 restraints weight = 8817.975| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5695 Z= 0.141 Angle : 0.682 13.410 7768 Z= 0.349 Chirality : 0.046 0.168 864 Planarity : 0.005 0.049 1002 Dihedral : 4.506 27.604 779 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.73 % Allowed : 22.47 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.88 (0.31), residues: 713 helix: -3.30 (0.84), residues: 21 sheet: 0.52 (0.34), residues: 236 loop : -1.09 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.016 0.001 TYR L 49 PHE 0.025 0.002 PHE A 456 TRP 0.015 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 5683) covalent geometry : angle 0.66722 / 0.34 ( 7742) SS BOND : bond 0.00806 / 0.41 ( 10) SS BOND : angle 2.07894 / 1.21 ( 20) hydrogen bonds : bond 0.03449 / 2.32 ( 144) hydrogen bonds : angle 5.52667 / 3.92 ( 402) link_BETA1-4 : bond 0.01273 / 0.67 ( 1) link_BETA1-4 : angle 2.88510 / 1.51 ( 3) link_NAG-ASN : bond 0.01162 / 0.61 ( 1) link_NAG-ASN : angle 4.18782 / 2.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.4700 (m-80) REVERT: L 134 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6651 (t) outliers start: 17 outliers final: 14 residues processed: 84 average time/residue: 0.1000 time to fit residues: 10.8327 Evaluate side-chains 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 66 optimal weight: 0.0670 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS ** L 147 GLN ** 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 = 0.3824 r_free = 0.3824 target = 0.158609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123541 restraints weight = 25168.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124059 restraints weight = 23164.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124912 restraints weight = 10395.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125959 restraints weight = 8785.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126077 restraints weight = 8519.959| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5695 Z= 0.128 Angle : 0.664 13.259 7768 Z= 0.340 Chirality : 0.046 0.168 864 Planarity : 0.005 0.096 1002 Dihedral : 4.446 27.558 779 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.05 % Allowed : 22.31 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.86 (0.31), residues: 713 helix: -3.26 (0.84), residues: 21 sheet: 0.54 (0.34), residues: 236 loop : -1.10 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.014 0.001 TYR L 91 PHE 0.015 0.001 PHE A 429 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 5683) covalent geometry : angle 0.65055 / 0.34 ( 7742) SS BOND : bond 0.00758 / 0.38 ( 10) SS BOND : angle 1.94237 / 1.13 ( 20) hydrogen bonds : bond 0.03184 / 2.14 ( 144) hydrogen bonds : angle 5.48480 / 3.90 ( 402) link_BETA1-4 : bond 0.01304 / 0.69 ( 1) link_BETA1-4 : angle 2.88619 / 1.51 ( 3) link_NAG-ASN : bond 0.01175 / 0.62 ( 1) link_NAG-ASN : angle 4.13515 / 2.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.219 Fit side-chains REVERT: A 495 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.4577 (m-80) REVERT: H 222 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7832 (ptm-80) REVERT: L 134 CYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6653 (t) outliers start: 19 outliers final: 15 residues processed: 84 average time/residue: 0.0934 time to fit residues: 10.0260 Evaluate side-chains 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 53 optimal weight: 0.3980 chunk 50 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** L 147 GLN ** 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 = 0.3857 r_free = 0.3857 target = 0.161846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128092 restraints weight = 22075.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129364 restraints weight = 23680.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129583 restraints weight = 8557.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129591 restraints weight = 7619.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129591 restraints weight = 7361.622| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5695 Z= 0.112 Angle : 0.635 12.912 7768 Z= 0.322 Chirality : 0.045 0.167 864 Planarity : 0.005 0.098 1002 Dihedral : 4.194 28.830 779 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.73 % Allowed : 22.47 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.69 (0.31), residues: 713 helix: -3.09 (0.88), residues: 21 sheet: 0.56 (0.33), residues: 249 loop : -0.95 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.011 0.001 TYR L 91 PHE 0.029 0.001 PHE A 456 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5683) covalent geometry : angle 0.62219 / 0.32 ( 7742) SS BOND : bond 0.00690 / 0.33 ( 10) SS BOND : angle 1.66633 / 0.95 ( 20) hydrogen bonds : bond 0.02902 / 1.95 ( 144) hydrogen bonds : angle 5.30704 / 3.80 ( 402) link_BETA1-4 : bond 0.01270 / 0.67 ( 1) link_BETA1-4 : angle 2.83026 / 1.48 ( 3) link_NAG-ASN : bond 0.01110 / 0.58 ( 1) link_NAG-ASN : angle 4.24808 / 2.22 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.213 Fit side-chains REVERT: A 495 TYR cc_start: 0.5603 (OUTLIER) cc_final: 0.4464 (m-80) REVERT: L 81 GLU cc_start: 0.7956 (pp20) cc_final: 0.7699 (pp20) REVERT: L 134 CYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6550 (t) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.0705 time to fit residues: 7.2315 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** L 147 GLN ** 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 = 0.3792 r_free = 0.3792 target = 0.155899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119841 restraints weight = 20435.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121602 restraints weight = 22964.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121262 restraints weight = 11834.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122298 restraints weight = 12208.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122469 restraints weight = 8985.617| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 5695 Z= 0.162 Angle : 0.699 13.534 7768 Z= 0.358 Chirality : 0.047 0.185 864 Planarity : 0.006 0.086 1002 Dihedral : 4.553 26.782 779 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.37 % Allowed : 21.99 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.76 (0.31), residues: 713 helix: -3.23 (0.87), residues: 21 sheet: 0.51 (0.34), residues: 254 loop : -1.01 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 509 TYR 0.019 0.002 TYR L 49 PHE 0.015 0.002 PHE A 562 TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 5683) covalent geometry : angle 0.68536 / 0.35 ( 7742) SS BOND : bond 0.00837 / 0.43 ( 10) SS BOND : angle 2.11740 / 1.27 ( 20) hydrogen bonds : bond 0.03614 / 2.42 ( 144) hydrogen bonds : angle 5.52843 / 3.92 ( 402) link_BETA1-4 : bond 0.01334 / 0.70 ( 1) link_BETA1-4 : angle 2.69565 / 1.41 ( 3) link_NAG-ASN : bond 0.01145 / 0.60 ( 1) link_NAG-ASN : angle 3.99299 / 2.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1395.89 seconds wall clock time: 24 minutes 50.61 seconds (1490.61 seconds total)