Starting phenix.real_space_refine on Tue Mar 3 13:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d48_27177/03_2026/8d48_27177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d48_27177/03_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_27177/03_2026/8d48_27177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_2026/8d48_27177.map" model { file = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_2026/8d48_27177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.31 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: 0.43 Conformation dependent library (CDL) restraints added in 427.1 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: 0.13 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: 0.62 Time building geometry restraints manager: 0.59 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 - 23.18: 3130 23.18 - 46.36: 260 46.36 - 69.54: 34 69.54 - 92.72: 6 92.72 - 115.90: 2 Dihedral angle restraints: 3432 sinusoidal: 1348 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 3429 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: 0.010 Normalize map: mean=0, sd=1: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 16.279 115.898 2072 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 covalent geometry : bond 0.00464 ( 5683) covalent geometry : angle 0.80680 ( 7742) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.55202 ( 20) hydrogen bonds : bond 0.20058 ( 144) hydrogen bonds : angle 6.89286 ( 402) link_BETA1-4 : bond 0.00201 ( 1) link_BETA1-4 : angle 4.03111 ( 3) link_NAG-ASN : bond 0.00896 ( 1) link_NAG-ASN : angle 4.52327 ( 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 : 0.137 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: 0.0848 time to fit residues: 9.2287 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 : 0.204 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4025 r_free = 0.4025 target = 0.175635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139818 restraints weight = 22187.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143756 restraints weight = 21209.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143221 restraints weight = 15723.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143992 restraints weight = 13108.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144373 restraints weight = 9483.730| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- 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: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1222 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= 0.165 Angle : 0.746 14.019 7768 Z= 0.378 Chirality : 0.047 0.171 864 Planarity : 0.007 0.108 1002 Dihedral : 6.576 62.070 821 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.05 % Allowed : 20.06 % Favored : 76.89 % 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: -1.02 (0.31), residues: 713 helix: -3.23 (0.86), residues: 21 sheet: 0.57 (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 0.025 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 covalent geometry : bond 0.00393 ( 5683) covalent geometry : angle 0.73227 ( 7742) SS BOND : bond 0.00885 ( 10) SS BOND : angle 1.69174 ( 20) hydrogen bonds : bond 0.04421 ( 144) hydrogen bonds : angle 6.00461 ( 402) link_BETA1-4 : bond 0.00595 ( 1) link_BETA1-4 : angle 4.65449 ( 3) link_NAG-ASN : bond 0.01515 ( 1) link_NAG-ASN : angle 4.28197 ( 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 95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.189 Fit side-chains REVERT: L 81 GLU cc_start: 0.8274 (pp20) cc_final: 0.8016 (pp20) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.0888 time to fit residues: 10.2508 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 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 208 CYS Chi-restraints excluded: chain H residue 210 VAL 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: 4.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 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 = 0.3861 r_free = 0.3861 target = 0.161655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128099 restraints weight = 27177.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129467 restraints weight = 25063.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129646 restraints weight = 8707.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129646 restraints weight = 8324.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129646 restraints weight = 8324.795| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 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 = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1417 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= 0.139 Angle : 0.695 13.824 7768 Z= 0.356 Chirality : 0.047 0.194 864 Planarity : 0.006 0.078 1002 Dihedral : 5.219 36.244 821 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.57 % Allowed : 20.71 % Favored : 76.73 % 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: -0.97 (0.31), residues: 713 helix: -3.13 (0.88), residues: 21 sheet: 0.62 (0.35), residues: 218 loop : -1.21 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 83 TYR 0.016 0.001 TYR L 49 PHE 0.013 0.001 PHE A 497 TRP 0.016 0.002 TRP A 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5683) covalent geometry : angle 0.68028 ( 7742) SS BOND : bond 0.00826 ( 10) SS BOND : angle 1.62350 ( 20) hydrogen bonds : bond 0.03883 ( 144) hydrogen bonds : angle 5.87684 ( 402) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 4.27958 ( 3) link_NAG-ASN : bond 0.01440 ( 1) link_NAG-ASN : angle 4.72286 ( 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 86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.203 Fit side-chains REVERT: H 156 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7768 (m) REVERT: L 81 GLU cc_start: 0.8266 (pp20) cc_final: 0.7944 (pp20) REVERT: L 96 TYR cc_start: 0.8453 (m-10) cc_final: 0.8252 (m-10) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.0882 time to fit residues: 9.2520 Evaluate side-chains 77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 156 SER Chi-restraints excluded: chain H residue 208 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3829 r_free = 0.3829 target = 0.158743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125179 restraints weight = 22974.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126242 restraints weight = 26659.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126926 restraints weight = 8603.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127613 restraints weight = 8678.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127613 restraints weight = 5993.975| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 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 = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1728 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= 0.161 Angle : 0.701 13.882 7768 Z= 0.360 Chirality : 0.047 0.169 864 Planarity : 0.006 0.062 1002 Dihedral : 5.195 33.103 821 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.53 % Allowed : 18.94 % Favored : 77.53 % 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: -1.02 (0.31), residues: 713 helix: -3.22 (0.86), residues: 21 sheet: 0.35 (0.34), residues: 238 loop : -1.17 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.019 0.001 TYR L 49 PHE 0.015 0.002 PHE A 562 TRP 0.018 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5683) covalent geometry : angle 0.68717 ( 7742) SS BOND : bond 0.00871 ( 10) SS BOND : angle 1.71976 ( 20) hydrogen bonds : bond 0.03952 ( 144) hydrogen bonds : angle 5.85317 ( 402) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 3.79806 ( 3) link_NAG-ASN : bond 0.01461 ( 1) link_NAG-ASN : angle 4.46766 ( 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 96 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.200 Fit side-chains REVERT: A 506 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: H 156 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7864 (m) REVERT: L 81 GLU cc_start: 0.8210 (pp20) cc_final: 0.7879 (pp20) outliers start: 22 outliers final: 17 residues processed: 89 average time/residue: 0.0854 time to fit residues: 9.7400 Evaluate side-chains 87 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3819 r_free = 0.3819 target = 0.157925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125693 restraints weight = 25560.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126985 restraints weight = 24113.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127034 restraints weight = 9956.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127032 restraints weight = 7683.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127031 restraints weight = 7350.917| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 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 = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1851 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= 0.156 Angle : 0.707 13.785 7768 Z= 0.363 Chirality : 0.046 0.165 864 Planarity : 0.005 0.053 1002 Dihedral : 5.149 30.282 821 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.49 % Allowed : 18.46 % 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: -1.03 (0.31), residues: 713 helix: -3.24 (0.87), residues: 21 sheet: 0.40 (0.34), residues: 236 loop : -1.20 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 222 TYR 0.018 0.001 TYR L 49 PHE 0.013 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 covalent geometry : bond 0.00374 ( 5683) covalent geometry : angle 0.69357 ( 7742) SS BOND : bond 0.00857 ( 10) SS BOND : angle 1.70334 ( 20) hydrogen bonds : bond 0.03835 ( 144) hydrogen bonds : angle 5.83571 ( 402) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 3.53021 ( 3) link_NAG-ASN : bond 0.01356 ( 1) link_NAG-ASN : angle 4.58807 ( 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 100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.203 Fit side-chains REVERT: H 156 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7854 (m) REVERT: L 81 GLU cc_start: 0.8254 (pp20) cc_final: 0.7913 (pp20) outliers start: 28 outliers final: 21 residues processed: 94 average time/residue: 0.0839 time to fit residues: 10.1339 Evaluate side-chains 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 557 LYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL 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 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 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 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: 1.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3786 r_free = 0.3786 target = 0.155158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133411 restraints weight = 16106.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132922 restraints weight = 22240.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130869 restraints weight = 8249.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131784 restraints weight = 5896.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132476 restraints weight = 3979.517| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 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 = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 5695 Z= 0.176 Angle : 0.746 13.952 7768 Z= 0.381 Chirality : 0.047 0.171 864 Planarity : 0.006 0.053 1002 Dihedral : 5.245 27.913 821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.65 % Allowed : 19.26 % Favored : 76.08 % 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: -1.05 (0.31), residues: 713 helix: -3.36 (0.84), residues: 21 sheet: 0.36 (0.34), residues: 238 loop : -1.20 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 222 TYR 0.020 0.002 TYR H 59 PHE 0.018 0.002 PHE A 562 TRP 0.019 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5683) covalent geometry : angle 0.73339 ( 7742) SS BOND : bond 0.00888 ( 10) SS BOND : angle 1.80604 ( 20) hydrogen bonds : bond 0.04057 ( 144) hydrogen bonds : angle 5.85814 ( 402) link_BETA1-4 : bond 0.00480 ( 1) link_BETA1-4 : angle 3.31503 ( 3) link_NAG-ASN : bond 0.01412 ( 1) link_NAG-ASN : angle 4.47504 ( 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 98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.208 Fit side-chains REVERT: L 81 GLU cc_start: 0.8159 (pp20) cc_final: 0.7832 (pp20) outliers start: 29 outliers final: 23 residues processed: 91 average time/residue: 0.0824 time to fit residues: 9.7133 Evaluate side-chains 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 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 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 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 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: 0.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3799 r_free = 0.3799 target = 0.156302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122041 restraints weight = 26444.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123047 restraints weight = 23723.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123357 restraints weight = 10470.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124083 restraints weight = 10368.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124632 restraints weight = 9706.280| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 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 = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5695 Z= 0.143 Angle : 0.703 13.789 7768 Z= 0.359 Chirality : 0.046 0.164 864 Planarity : 0.005 0.050 1002 Dihedral : 5.108 27.249 821 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.17 % Allowed : 19.10 % Favored : 76.73 % 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: -1.00 (0.31), residues: 713 helix: -3.36 (0.84), residues: 21 sheet: 0.48 (0.34), residues: 236 loop : -1.21 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 222 TYR 0.017 0.001 TYR L 91 PHE 0.012 0.002 PHE A 562 TRP 0.018 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5683) covalent geometry : angle 0.69011 ( 7742) SS BOND : bond 0.00828 ( 10) SS BOND : angle 1.67575 ( 20) hydrogen bonds : bond 0.03618 ( 144) hydrogen bonds : angle 5.76273 ( 402) link_BETA1-4 : bond 0.00442 ( 1) link_BETA1-4 : angle 3.23569 ( 3) link_NAG-ASN : bond 0.01305 ( 1) link_NAG-ASN : angle 4.56248 ( 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 95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.155 Fit side-chains REVERT: H 222 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.8052 (ptm-80) REVERT: L 81 GLU cc_start: 0.8243 (pp20) cc_final: 0.7925 (pp20) outliers start: 26 outliers final: 25 residues processed: 88 average time/residue: 0.0783 time to fit residues: 8.8481 Evaluate side-chains 93 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 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 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 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 150 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3781 r_free = 0.3781 target = 0.155091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133693 restraints weight = 15158.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132764 restraints weight = 20759.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131309 restraints weight = 7855.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132095 restraints weight = 5962.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132183 restraints weight = 3941.772| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2424 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= 0.160 Angle : 0.708 13.872 7768 Z= 0.364 Chirality : 0.047 0.170 864 Planarity : 0.006 0.096 1002 Dihedral : 5.100 28.434 821 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.33 % Allowed : 19.58 % Favored : 76.08 % 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: -1.03 (0.31), residues: 713 helix: -3.34 (0.86), residues: 21 sheet: 0.29 (0.33), residues: 259 loop : -1.20 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 222 TYR 0.019 0.001 TYR L 49 PHE 0.027 0.002 PHE A 456 TRP 0.018 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5683) covalent geometry : angle 0.69285 ( 7742) SS BOND : bond 0.00881 ( 10) SS BOND : angle 2.09595 ( 20) hydrogen bonds : bond 0.03722 ( 144) hydrogen bonds : angle 5.70439 ( 402) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 3.18353 ( 3) link_NAG-ASN : bond 0.01326 ( 1) link_NAG-ASN : angle 4.49583 ( 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 98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.203 Fit side-chains REVERT: L 81 GLU cc_start: 0.8140 (pp20) cc_final: 0.7828 (pp20) outliers start: 27 outliers final: 25 residues processed: 91 average time/residue: 0.0859 time to fit residues: 9.9897 Evaluate side-chains 94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3795 r_free = 0.3795 target = 0.156467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122385 restraints weight = 25079.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123218 restraints weight = 23929.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123377 restraints weight = 11428.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123921 restraints weight = 10017.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123943 restraints weight = 8649.855| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 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 = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5695 Z= 0.137 Angle : 0.686 13.722 7768 Z= 0.353 Chirality : 0.046 0.160 864 Planarity : 0.006 0.096 1002 Dihedral : 4.912 27.980 821 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.53 % Allowed : 20.87 % Favored : 75.60 % 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: -0.93 (0.31), residues: 713 helix: -3.32 (0.86), residues: 21 sheet: 0.53 (0.34), residues: 236 loop : -1.17 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 222 TYR 0.016 0.001 TYR L 91 PHE 0.012 0.001 PHE A 497 TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5683) covalent geometry : angle 0.67007 ( 7742) SS BOND : bond 0.00792 ( 10) SS BOND : angle 2.04874 ( 20) hydrogen bonds : bond 0.03372 ( 144) hydrogen bonds : angle 5.62240 ( 402) link_BETA1-4 : bond 0.00451 ( 1) link_BETA1-4 : angle 3.08438 ( 3) link_NAG-ASN : bond 0.01306 ( 1) link_NAG-ASN : angle 4.53456 ( 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 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.146 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.0902 time to fit residues: 9.6326 Evaluate side-chains 84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU 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 107 THR 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 50 TRP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 20.0000 chunk 66 optimal weight: 0.0030 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3960 r_free = 0.3960 target = 0.169508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135092 restraints weight = 21283.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136903 restraints weight = 23035.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138084 restraints weight = 14660.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137780 restraints weight = 13933.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138809 restraints weight = 12715.132| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 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 = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2537 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= 0.132 Angle : 0.680 13.657 7768 Z= 0.349 Chirality : 0.046 0.168 864 Planarity : 0.006 0.088 1002 Dihedral : 4.860 28.117 821 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.73 % Allowed : 21.35 % 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: -0.88 (0.31), residues: 713 helix: -3.25 (0.88), residues: 21 sheet: 0.57 (0.35), residues: 236 loop : -1.14 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.015 0.001 TYR L 49 PHE 0.026 0.001 PHE A 456 TRP 0.016 0.002 TRP A 436 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5683) covalent geometry : angle 0.66504 ( 7742) SS BOND : bond 0.00773 ( 10) SS BOND : angle 1.95502 ( 20) hydrogen bonds : bond 0.03300 ( 144) hydrogen bonds : angle 5.55690 ( 402) link_BETA1-4 : bond 0.00420 ( 1) link_BETA1-4 : angle 3.02185 ( 3) link_NAG-ASN : bond 0.01290 ( 1) link_NAG-ASN : angle 4.51559 ( 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 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.213 Fit side-chains outliers start: 17 outliers final: 17 residues processed: 81 average time/residue: 0.0961 time to fit residues: 9.8890 Evaluate side-chains 84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 557 LYS 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 107 THR 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 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR 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: 3.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3796 r_free = 0.3796 target = 0.156399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120002 restraints weight = 20447.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121838 restraints weight = 22184.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121755 restraints weight = 14098.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122068 restraints weight = 12962.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122325 restraints weight = 10519.097| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5695 Z= 0.140 Angle : 0.684 13.764 7768 Z= 0.352 Chirality : 0.046 0.171 864 Planarity : 0.006 0.089 1002 Dihedral : 4.846 28.424 821 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.37 % Allowed : 21.03 % Favored : 75.60 % 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: -0.87 (0.31), residues: 713 helix: -3.26 (0.88), residues: 21 sheet: 0.69 (0.35), residues: 231 loop : -1.18 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.016 0.001 TYR L 49 PHE 0.014 0.001 PHE A 497 TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5683) covalent geometry : angle 0.66924 ( 7742) SS BOND : bond 0.00792 ( 10) SS BOND : angle 1.99863 ( 20) hydrogen bonds : bond 0.03381 ( 144) hydrogen bonds : angle 5.56117 ( 402) link_BETA1-4 : bond 0.00434 ( 1) link_BETA1-4 : angle 2.95984 ( 3) link_NAG-ASN : bond 0.01275 ( 1) link_NAG-ASN : angle 4.45256 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.55 seconds wall clock time: 22 minutes 43.30 seconds (1363.30 seconds total)