Starting phenix.real_space_refine on Thu Jul 2 02:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2026/7ure_26710.cif" } resolution = 3.19 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= 0.005 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 3566 2.51 5 N 895 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3465 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DNP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' ZN': 1, 'AJP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2849 SG CYS A 370 54.825 29.237 18.480 1.00101.61 S ATOM 2896 SG CYS A 376 53.706 28.652 22.060 1.00110.68 S Time building chain proxies: 1.32, per 1000 atoms: 0.24 Number of scatterers: 5450 At special positions: 0 Unit cell: (97.11, 70.55, 97.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 953 8.00 N 895 7.00 C 3566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 212 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 151.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 376 " 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 50.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 5 through 43 removed outlier: 4.015A pdb=" N GLN A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Proline residue: A 20 - end of helix removed outlier: 5.369A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 116 through 144 removed outlier: 5.316A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 186 through 210 removed outlier: 3.719A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 265 removed outlier: 3.616A pdb=" N GLY A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.554A pdb=" N VAL A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 removed outlier: 4.510A pdb=" N ASN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.691A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 367 Processing helix chain 'A' and resid 388 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 439 through 456 Processing helix chain 'L' and resid 99 through 103 removed outlier: 4.091A pdb=" N PHE L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.185A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.679A pdb=" N GLU A 276 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 27 removed outlier: 4.126A pdb=" N GLN L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER L 87 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 92 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.299A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU L 53 " --> pdb=" O TYR L 69 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR L 69 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.728A pdb=" N TYR H 113 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET H 53 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER H 76 " --> pdb=" O ASN H 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.728A pdb=" N TYR H 113 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.502A pdb=" N TRP B 218 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 204 " --> pdb=" O THR B 216 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 900 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: 0.57 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 5 1.20 - 1.40: 2365 1.40 - 1.60: 3182 1.60 - 1.79: 21 1.79 - 1.99: 39 Bond restraints: 5612 Sorted by residual: bond pdb=" C07 AJP A 501 " pdb=" C08 AJP A 501 " ideal model delta sigma weight residual 1.550 1.991 -0.441 2.00e-02 2.50e+03 4.86e+02 bond pdb=" C01 AJP A 501 " pdb=" C02 AJP A 501 " ideal model delta sigma weight residual 1.521 1.950 -0.429 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C08 AJP A 501 " pdb=" O09 AJP A 501 " ideal model delta sigma weight residual 1.410 1.002 0.408 2.00e-02 2.50e+03 4.16e+02 bond pdb=" C05 AJP A 501 " pdb=" O09 AJP A 501 " ideal model delta sigma weight residual 1.407 1.803 -0.396 2.00e-02 2.50e+03 3.92e+02 bond pdb=" C02 AJP A 501 " pdb=" C03 AJP A 501 " ideal model delta sigma weight residual 1.525 1.130 0.395 2.00e-02 2.50e+03 3.91e+02 ... (remaining 5607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 7561 3.41 - 6.82: 55 6.82 - 10.22: 9 10.22 - 13.63: 3 13.63 - 17.04: 2 Bond angle restraints: 7630 Sorted by residual: angle pdb=" C2 PAM B 601 " pdb=" C1 PAM B 601 " pdb=" O1 PAM B 601 " ideal model delta sigma weight residual 115.96 98.92 17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C11 AJP A 501 " pdb=" C12 AJP A 501 " pdb=" C81 AJP A 501 " ideal model delta sigma weight residual 114.35 100.70 13.65 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C03 AJP A 501 " pdb=" C02 AJP A 501 " pdb=" C85 AJP A 501 " ideal model delta sigma weight residual 109.14 122.46 -13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C04 AJP A 501 " pdb=" C05 AJP A 501 " pdb=" O84 AJP A 501 " ideal model delta sigma weight residual 111.01 122.20 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C06 AJP A 501 " pdb=" C07 AJP A 501 " pdb=" C12 AJP A 501 " ideal model delta sigma weight residual 120.30 130.92 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 7625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 2948 21.30 - 42.60: 211 42.60 - 63.90: 21 63.90 - 85.20: 3 85.20 - 106.50: 4 Dihedral angle restraints: 3187 sinusoidal: 1225 harmonic: 1962 Sorted by residual: dihedral pdb=" C12 AJP A 501 " pdb=" C13 AJP A 501 " pdb=" C14 AJP A 501 " pdb=" C15 AJP A 501 " ideal model delta sinusoidal sigma weight residual -53.33 53.17 -106.50 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C16 AJP A 501 " pdb=" C17 AJP A 501 " pdb=" C18 AJP A 501 " pdb=" C19 AJP A 501 " ideal model delta sinusoidal sigma weight residual 54.20 -51.31 105.51 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -56.08 -29.92 1 1.00e+01 1.00e-02 1.28e+01 ... (remaining 3184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.102: 832 1.102 - 2.205: 0 2.205 - 3.307: 0 3.307 - 4.409: 2 4.409 - 5.512: 19 Chirality restraints: 853 Sorted by residual: chirality pdb=" C15 AJP A 501 " pdb=" C14 AJP A 501 " pdb=" C16 AJP A 501 " pdb=" C20 AJP A 501 " both_signs ideal model delta sigma weight residual False -2.42 3.09 -5.51 2.00e-01 2.50e+01 7.59e+02 chirality pdb=" C20 AJP A 501 " pdb=" C15 AJP A 501 " pdb=" C19 AJP A 501 " pdb=" C21 AJP A 501 " both_signs ideal model delta sigma weight residual False 2.96 -2.52 5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C16 AJP A 501 " pdb=" C11 AJP A 501 " pdb=" C15 AJP A 501 " pdb=" C17 AJP A 501 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.47 2.00e-01 2.50e+01 7.47e+02 ... (remaining 850 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 310 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ASN A 310 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN A 310 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 311 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 309 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ASN A 309 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 309 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 216 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.028 5.00e-02 4.00e+02 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 84 2.67 - 3.23: 5166 3.23 - 3.79: 8435 3.79 - 4.34: 11495 4.34 - 4.90: 19542 Nonbonded interactions: 44722 Sorted by model distance: nonbonded pdb=" O LEU A 319 " pdb=" OG SER A 323 " model vdw 2.118 3.040 nonbonded pdb=" O33 AJP A 501 " pdb=" O40 AJP A 501 " model vdw 2.265 3.040 nonbonded pdb=" O ARG A 90 " pdb=" NH1 ARG A 95 " model vdw 2.276 3.120 nonbonded pdb=" O PHE A 340 " pdb=" ND1 HIS A 341 " model vdw 2.276 3.120 nonbonded pdb=" ND1 HIS A 53 " pdb=" OH TYR A 176 " model vdw 2.315 3.120 ... (remaining 44717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.018 0.441 5621 Z= 0.882 Angle : 0.781 17.041 7640 Z= 0.350 Chirality : 0.778 5.512 853 Planarity : 0.005 0.049 921 Dihedral : 14.255 106.503 1918 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.30), residues: 663 helix: -0.41 (0.25), residues: 331 sheet: -2.23 (0.46), residues: 125 loop : -2.62 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.016 0.002 TYR A 83 PHE 0.010 0.001 PHE A 268 TRP 0.007 0.001 TRP H 66 HIS 0.005 0.001 HIS L 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01736 / 0.87 ( 5612) covalent geometry : angle 0.78063 / 0.35 ( 7630) SS BOND : bond 0.00159 / 0.11 ( 5) SS BOND : angle 0.71560 / 0.41 ( 10) hydrogen bonds : bond 0.13546 / 8.73 ( 313) hydrogen bonds : angle 6.66551 / 4.95 ( 900) metal coordination : bond 0.14268 / 7.10 ( 3) Misc. bond : bond 0.10044 / 5.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8161 (t80) cc_final: 0.7925 (t80) REVERT: A 201 LEU cc_start: 0.7964 (mt) cc_final: 0.7760 (mm) REVERT: A 407 TYR cc_start: 0.8170 (t80) cc_final: 0.7482 (t80) REVERT: A 434 TRP cc_start: 0.8299 (m-10) cc_final: 0.8018 (m-10) REVERT: A 452 TYR cc_start: 0.6613 (t80) cc_final: 0.6403 (t80) REVERT: L 116 TYR cc_start: 0.9007 (m-80) cc_final: 0.8725 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0752 time to fit residues: 7.8183 Evaluate side-chains 73 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 71 HIS A 91 HIS A 121 HIS A 127 GLN A 181 GLN A 315 ASN A 394 ASN L 96 ASN L 111 HIS H 22 GLN H 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114846 restraints weight = 6012.323| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.34 r_work: 0.3065 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5621 Z= 0.136 Angle : 1.102 32.685 7640 Z= 0.421 Chirality : 0.126 2.231 853 Planarity : 0.005 0.044 921 Dihedral : 5.988 57.875 750 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.69 % Allowed : 9.66 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.74 (0.32), residues: 663 helix: 0.99 (0.27), residues: 328 sheet: -1.64 (0.45), residues: 135 loop : -2.07 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.017 0.002 TYR A 83 PHE 0.008 0.001 PHE A 268 TRP 0.007 0.001 TRP H 66 HIS 0.007 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5612) covalent geometry : angle 1.10209 / 0.42 ( 7630) SS BOND : bond 0.00270 / 0.13 ( 5) SS BOND : angle 0.52687 / 0.38 ( 10) hydrogen bonds : bond 0.03347 / 2.16 ( 313) hydrogen bonds : angle 4.94847 / 3.60 ( 900) metal coordination : bond 0.00107 / 0.05 ( 3) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7877 (t80) cc_final: 0.7645 (t80) REVERT: A 112 MET cc_start: 0.5789 (tmm) cc_final: 0.5247 (ttm) REVERT: A 341 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7159 (p-80) REVERT: A 342 LEU cc_start: 0.7540 (tp) cc_final: 0.7194 (tp) REVERT: A 434 TRP cc_start: 0.7714 (m-10) cc_final: 0.7320 (m-10) REVERT: L 116 TYR cc_start: 0.9200 (m-80) cc_final: 0.8902 (m-80) REVERT: B 217 CYS cc_start: 0.7437 (m) cc_final: 0.7185 (m) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.0642 time to fit residues: 5.8353 Evaluate side-chains 65 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN ** H 123 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.151946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116435 restraints weight = 5908.449| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.25 r_work: 0.3114 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5621 Z= 0.122 Angle : 1.076 33.616 7640 Z= 0.407 Chirality : 0.125 2.195 853 Planarity : 0.004 0.043 921 Dihedral : 5.555 55.148 750 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.38 % Allowed : 11.38 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.02 (0.33), residues: 663 helix: 1.65 (0.28), residues: 327 sheet: -1.36 (0.44), residues: 135 loop : -1.79 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.021 0.002 TYR L 52 PHE 0.008 0.001 PHE A 248 TRP 0.006 0.001 TRP A 74 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5612) covalent geometry : angle 1.07640 / 0.41 ( 7630) SS BOND : bond 0.00232 / 0.11 ( 5) SS BOND : angle 0.50628 / 0.37 ( 10) hydrogen bonds : bond 0.03029 / 1.96 ( 313) hydrogen bonds : angle 4.56916 / 3.33 ( 900) metal coordination : bond 0.00101 / 0.05 ( 3) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7866 (t80) cc_final: 0.7629 (t80) REVERT: A 186 SER cc_start: 0.8233 (t) cc_final: 0.7688 (p) REVERT: A 341 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7242 (p-80) REVERT: A 342 LEU cc_start: 0.7609 (tp) cc_final: 0.7303 (tp) REVERT: A 388 LEU cc_start: 0.7747 (tt) cc_final: 0.7107 (pp) REVERT: L 116 TYR cc_start: 0.9207 (m-80) cc_final: 0.8929 (m-80) REVERT: H 93 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6835 (mtm180) REVERT: B 217 CYS cc_start: 0.7299 (m) cc_final: 0.7071 (m) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.0816 time to fit residues: 7.6510 Evaluate side-chains 69 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 47 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS ** H 123 HIS ** 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 = 0.3752 r_free = 0.3752 target = 0.154546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119476 restraints weight = 5942.197| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.14 r_work: 0.3205 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5621 Z= 0.114 Angle : 1.077 33.392 7640 Z= 0.407 Chirality : 0.123 2.172 853 Planarity : 0.004 0.040 921 Dihedral : 5.253 58.475 750 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.90 % Allowed : 11.21 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.40 (0.34), residues: 663 helix: 1.97 (0.28), residues: 327 sheet: -1.10 (0.44), residues: 134 loop : -1.61 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.017 0.001 TYR A 83 PHE 0.007 0.001 PHE A 248 TRP 0.006 0.001 TRP A 74 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5612) covalent geometry : angle 1.07803 / 0.41 ( 7630) SS BOND : bond 0.00199 / 0.10 ( 5) SS BOND : angle 0.42658 / 0.31 ( 10) hydrogen bonds : bond 0.02887 / 1.87 ( 313) hydrogen bonds : angle 4.39263 / 3.21 ( 900) metal coordination : bond 0.00079 / 0.04 ( 3) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8170 (t80) cc_final: 0.7932 (t80) REVERT: A 112 MET cc_start: 0.5936 (tmm) cc_final: 0.5585 (ttm) REVERT: A 186 SER cc_start: 0.8498 (t) cc_final: 0.7954 (p) REVERT: A 318 ARG cc_start: 0.6430 (mtp85) cc_final: 0.6188 (mtt-85) REVERT: A 341 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7322 (p-80) REVERT: A 388 LEU cc_start: 0.7811 (tt) cc_final: 0.7113 (pp) REVERT: H 93 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.7262 (mtm180) REVERT: B 217 CYS cc_start: 0.7499 (m) cc_final: 0.7275 (m) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.0854 time to fit residues: 8.1094 Evaluate side-chains 69 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS H 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117973 restraints weight = 6101.372| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.17 r_work: 0.3193 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5621 Z= 0.129 Angle : 1.075 33.876 7640 Z= 0.407 Chirality : 0.124 2.235 853 Planarity : 0.004 0.041 921 Dihedral : 5.075 57.275 750 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.72 % Allowed : 12.59 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.55 (0.34), residues: 663 helix: 1.94 (0.28), residues: 333 sheet: -0.89 (0.45), residues: 134 loop : -1.46 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.018 0.002 TYR A 83 PHE 0.009 0.001 PHE A 248 TRP 0.007 0.001 TRP A 74 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 5612) covalent geometry : angle 1.07576 / 0.41 ( 7630) SS BOND : bond 0.00185 / 0.09 ( 5) SS BOND : angle 0.40616 / 0.29 ( 10) hydrogen bonds : bond 0.03003 / 1.95 ( 313) hydrogen bonds : angle 4.36752 / 3.19 ( 900) metal coordination : bond 0.00096 / 0.05 ( 3) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8088 (t80) cc_final: 0.7837 (t80) REVERT: A 112 MET cc_start: 0.5927 (tmm) cc_final: 0.5535 (ttm) REVERT: A 341 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7257 (p-80) REVERT: A 388 LEU cc_start: 0.7835 (tt) cc_final: 0.7110 (pp) REVERT: H 93 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7184 (mtm180) REVERT: B 217 CYS cc_start: 0.7436 (m) cc_final: 0.7203 (m) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.0808 time to fit residues: 7.1523 Evaluate side-chains 69 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120562 restraints weight = 6005.528| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.25 r_work: 0.3222 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5621 Z= 0.100 Angle : 1.059 33.388 7640 Z= 0.396 Chirality : 0.122 2.182 853 Planarity : 0.004 0.039 921 Dihedral : 4.473 49.746 750 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.55 % Allowed : 13.28 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.83 (0.34), residues: 663 helix: 2.19 (0.28), residues: 333 sheet: -0.76 (0.44), residues: 134 loop : -1.38 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 453 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP H 128 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 5612) covalent geometry : angle 1.05971 / 0.40 ( 7630) SS BOND : bond 0.00177 / 0.09 ( 5) SS BOND : angle 0.38439 / 0.26 ( 10) hydrogen bonds : bond 0.02673 / 1.74 ( 313) hydrogen bonds : angle 4.21461 / 3.08 ( 900) metal coordination : bond 0.00050 / 0.02 ( 3) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8188 (t80) cc_final: 0.7985 (t80) REVERT: A 109 MET cc_start: 0.7613 (mmt) cc_final: 0.7388 (mmp) REVERT: A 112 MET cc_start: 0.6313 (tmm) cc_final: 0.5707 (ttm) REVERT: A 186 SER cc_start: 0.8480 (t) cc_final: 0.7936 (p) REVERT: A 276 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 288 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 341 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7322 (p-80) REVERT: A 388 LEU cc_start: 0.7830 (tt) cc_final: 0.7201 (pp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0835 time to fit residues: 8.4797 Evaluate side-chains 74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123728 restraints weight = 6190.183| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.97 r_work: 0.3332 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5621 Z= 0.171 Angle : 1.091 33.913 7640 Z= 0.419 Chirality : 0.123 2.213 853 Planarity : 0.004 0.040 921 Dihedral : 4.739 48.907 750 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.72 % Allowed : 14.48 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.67 (0.33), residues: 663 helix: 2.00 (0.28), residues: 327 sheet: -0.61 (0.45), residues: 134 loop : -1.40 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.018 0.002 TYR A 83 PHE 0.011 0.001 PHE A 248 TRP 0.011 0.001 TRP A 74 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 5612) covalent geometry : angle 1.09100 / 0.42 ( 7630) SS BOND : bond 0.00205 / 0.10 ( 5) SS BOND : angle 0.72642 / 0.46 ( 10) hydrogen bonds : bond 0.03311 / 2.15 ( 313) hydrogen bonds : angle 4.53320 / 3.30 ( 900) metal coordination : bond 0.00164 / 0.08 ( 3) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8392 (t80) cc_final: 0.8129 (t80) REVERT: A 341 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7186 (p-80) REVERT: A 407 TYR cc_start: 0.8506 (t80) cc_final: 0.7992 (t80) REVERT: A 434 TRP cc_start: 0.8287 (m-10) cc_final: 0.7965 (m-10) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.0823 time to fit residues: 8.0622 Evaluate side-chains 71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 39 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118733 restraints weight = 5955.018| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.14 r_work: 0.3198 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5621 Z= 0.122 Angle : 1.091 33.470 7640 Z= 0.414 Chirality : 0.123 2.187 853 Planarity : 0.004 0.038 921 Dihedral : 4.423 44.398 750 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.38 % Allowed : 14.48 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.33), residues: 663 helix: 2.12 (0.28), residues: 333 sheet: -0.53 (0.45), residues: 133 loop : -1.34 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 391 TYR 0.018 0.001 TYR A 452 PHE 0.008 0.001 PHE A 248 TRP 0.007 0.001 TRP A 74 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5612) covalent geometry : angle 1.09092 / 0.41 ( 7630) SS BOND : bond 0.00236 / 0.12 ( 5) SS BOND : angle 0.76850 / 0.47 ( 10) hydrogen bonds : bond 0.02932 / 1.90 ( 313) hydrogen bonds : angle 4.39721 / 3.21 ( 900) metal coordination : bond 0.00087 / 0.04 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8100 (t80) cc_final: 0.7855 (t80) REVERT: A 112 MET cc_start: 0.5670 (tmm) cc_final: 0.5273 (ttm) REVERT: A 341 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7222 (p-80) REVERT: A 388 LEU cc_start: 0.7737 (tt) cc_final: 0.7131 (pp) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.0759 time to fit residues: 7.0875 Evaluate side-chains 74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 39 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 21 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118759 restraints weight = 5995.876| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.14 r_work: 0.3198 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5621 Z= 0.124 Angle : 1.088 33.454 7640 Z= 0.412 Chirality : 0.122 2.182 853 Planarity : 0.004 0.043 921 Dihedral : 4.287 38.078 750 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 15.00 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.33), residues: 663 helix: 2.15 (0.28), residues: 333 sheet: -0.45 (0.45), residues: 135 loop : -1.21 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 248 TRP 0.007 0.001 TRP A 74 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 5612) covalent geometry : angle 1.08841 / 0.41 ( 7630) SS BOND : bond 0.00262 / 0.13 ( 5) SS BOND : angle 0.61439 / 0.39 ( 10) hydrogen bonds : bond 0.02938 / 1.91 ( 313) hydrogen bonds : angle 4.36986 / 3.19 ( 900) metal coordination : bond 0.00095 / 0.05 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8081 (t80) cc_final: 0.7843 (t80) REVERT: A 112 MET cc_start: 0.5646 (tmm) cc_final: 0.5237 (ttm) REVERT: A 341 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7203 (p-80) REVERT: A 388 LEU cc_start: 0.7725 (tt) cc_final: 0.7105 (pp) REVERT: H 44 SER cc_start: 0.8252 (t) cc_final: 0.7799 (p) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.0765 time to fit residues: 7.4224 Evaluate side-chains 74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123599 restraints weight = 6152.543| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.96 r_work: 0.3319 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5621 Z= 0.170 Angle : 1.107 33.769 7640 Z= 0.426 Chirality : 0.123 2.207 853 Planarity : 0.004 0.038 921 Dihedral : 4.475 32.754 750 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.55 % Allowed : 14.48 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.83 (0.33), residues: 663 helix: 2.03 (0.28), residues: 327 sheet: -0.32 (0.46), residues: 134 loop : -1.29 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.019 0.002 TYR L 52 PHE 0.011 0.001 PHE A 248 TRP 0.010 0.001 TRP A 74 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 5612) covalent geometry : angle 1.10784 / 0.43 ( 7630) SS BOND : bond 0.00306 / 0.15 ( 5) SS BOND : angle 0.65047 / 0.41 ( 10) hydrogen bonds : bond 0.03341 / 2.16 ( 313) hydrogen bonds : angle 4.52592 / 3.30 ( 900) metal coordination : bond 0.00167 / 0.08 ( 3) Misc. bond : bond 0.00017 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.187 Fit side-chains REVERT: A 62 PHE cc_start: 0.8418 (t80) cc_final: 0.8161 (t80) REVERT: A 112 MET cc_start: 0.6129 (tmm) cc_final: 0.5769 (ttm) REVERT: A 341 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7199 (p-80) REVERT: A 388 LEU cc_start: 0.7751 (tt) cc_final: 0.7123 (pp) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.0720 time to fit residues: 6.7441 Evaluate side-chains 70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 59 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120091 restraints weight = 6066.656| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.17 r_work: 0.3216 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5621 Z= 0.110 Angle : 1.081 33.239 7640 Z= 0.408 Chirality : 0.122 2.174 853 Planarity : 0.004 0.040 921 Dihedral : 4.167 28.709 750 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 15.00 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.13 (0.34), residues: 663 helix: 2.19 (0.28), residues: 333 sheet: -0.15 (0.46), residues: 134 loop : -1.14 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.018 0.001 TYR A 83 PHE 0.009 0.001 PHE A 451 TRP 0.005 0.001 TRP A 74 HIS 0.003 0.001 HIS L 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5612) covalent geometry : angle 1.08129 / 0.41 ( 7630) SS BOND : bond 0.00294 / 0.15 ( 5) SS BOND : angle 0.57709 / 0.38 ( 10) hydrogen bonds : bond 0.02812 / 1.83 ( 313) hydrogen bonds : angle 4.34195 / 3.18 ( 900) metal coordination : bond 0.00066 / 0.03 ( 3) Misc. bond : bond 0.00009 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.11 seconds wall clock time: 24 minutes 50.97 seconds (1490.97 seconds total)