Starting phenix.real_space_refine on Thu Sep 10 22:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.map" model { file = "/net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi8_66900/09_2026/9xi8_66900.cif" } resolution = 3.45 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= 0.001 sd= 0.051 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 19 5.16 5 C 2912 2.51 5 N 769 2.21 5 O 922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4622 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1645 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1671 Chain: "L" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1570 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1407 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Time building chain proxies: 1.37, per 1000 atoms: 0.30 Number of scatterers: 4622 At special positions: 0 Unit cell: (68.64, 91.08, 113.52, 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 19 16.00 O 922 8.00 N 769 7.00 C 2912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 498 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 153.5 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 14 sheets defined 10.0% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.701A pdb=" N VAL A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 396 through 402 removed outlier: 4.397A pdb=" N ARG A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 402 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 475 through 478 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.641A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.641A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER H 100 " --> pdb=" O MET H 111 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N MET H 111 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.859A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS H 151 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.948A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.476A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.476A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.270A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.270A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.676A pdb=" N ALA L 152 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN L 199 " --> pdb=" O ALA L 152 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.867A pdb=" N SER A 385 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 387 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN A 428 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 365 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 435 through 440 removed outlier: 3.534A pdb=" N TYR A 437 " --> pdb=" O TYR A 468 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 437 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: 0.67 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1461 1.34 - 1.46: 1137 1.46 - 1.58: 2116 1.58 - 1.71: 0 1.71 - 1.83: 26 Bond restraints: 4740 Sorted by residual: bond pdb=" N ILE H 52 " pdb=" CA ILE H 52 " ideal model delta sigma weight residual 1.460 1.494 -0.034 9.30e-03 1.16e+04 1.32e+01 bond pdb=" N ILE H 54 " pdb=" CA ILE H 54 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N ASP A 457 " pdb=" CA ASP A 457 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.62e+00 bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.17e+00 bond pdb=" N THR H 57 " pdb=" CA THR H 57 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.95e+00 ... (remaining 4735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6237 1.57 - 3.14: 194 3.14 - 4.71: 27 4.71 - 6.28: 11 6.28 - 7.85: 4 Bond angle restraints: 6473 Sorted by residual: angle pdb=" CA THR H 57 " pdb=" C THR H 57 " pdb=" O THR H 57 " ideal model delta sigma weight residual 121.87 118.04 3.83 1.16e+00 7.43e-01 1.09e+01 angle pdb=" CA SER A 455 " pdb=" C SER A 455 " pdb=" O SER A 455 " ideal model delta sigma weight residual 121.55 118.16 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" O ILE H 54 " ideal model delta sigma weight residual 120.95 117.84 3.11 1.04e+00 9.25e-01 8.96e+00 angle pdb=" N ASN L 175 " pdb=" CA ASN L 175 " pdb=" CB ASN L 175 " ideal model delta sigma weight residual 113.65 109.26 4.39 1.47e+00 4.63e-01 8.92e+00 angle pdb=" CA LYS L 107 " pdb=" CB LYS L 107 " pdb=" CG LYS L 107 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.64e+00 ... (remaining 6468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2542 17.83 - 35.67: 226 35.67 - 53.50: 56 53.50 - 71.34: 6 71.34 - 89.17: 4 Dihedral angle restraints: 2834 sinusoidal: 1051 harmonic: 1783 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 160.92 -67.92 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CA TYR A 437 " pdb=" C TYR A 437 " pdb=" N TYR A 438 " pdb=" CA TYR A 438 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LYS L 171 " pdb=" C LYS L 171 " pdb=" N GLN L 172 " pdb=" CA GLN L 172 " ideal model delta harmonic sigma weight residual 180.00 163.68 16.32 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 485 0.036 - 0.073: 158 0.073 - 0.109: 60 0.109 - 0.146: 27 0.146 - 0.182: 4 Chirality restraints: 734 Sorted by residual: chirality pdb=" CA ILE H 52 " pdb=" N ILE H 52 " pdb=" C ILE H 52 " pdb=" CB ILE H 52 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ASP H 112 " pdb=" N ASP H 112 " pdb=" C ASP H 112 " pdb=" CB ASP H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 731 not shown) Planarity restraints: 831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLY L 112 " 0.076 2.00e-02 2.50e+03 pdb=" O GLY L 112 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN L 113 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 51 " -0.009 2.00e-02 2.50e+03 1.10e-02 2.43e+00 pdb=" CG TYR L 51 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR L 51 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 51 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR L 51 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 51 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 51 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 51 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 113 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO L 114 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " 0.020 5.00e-02 4.00e+02 ... (remaining 828 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 635 2.76 - 3.29: 4232 3.29 - 3.83: 7365 3.83 - 4.36: 8342 4.36 - 4.90: 15114 Nonbonded interactions: 35688 Sorted by model distance: nonbonded pdb=" OH TYR H 102 " pdb=" OD2 ASP L 34 " model vdw 2.224 3.040 nonbonded pdb=" O LYS H 13 " pdb=" OG SER H 16 " model vdw 2.308 3.040 nonbonded pdb=" OG SER H 35 " pdb=" OD2 ASP H 99 " model vdw 2.402 3.040 nonbonded pdb=" NH2 ARG H 50 " pdb=" OD2 ASP H 99 " model vdw 2.410 3.120 nonbonded pdb=" OD2 ASP L 94 " pdb=" OG SER L 96 " model vdw 2.421 3.040 ... (remaining 35683 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.004 0.035 4747 Z= 0.238 Angle : 0.668 7.850 6489 Z= 0.379 Chirality : 0.046 0.182 734 Planarity : 0.004 0.044 831 Dihedral : 14.467 89.171 1674 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.19 % Allowed : 23.85 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.35), residues: 608 helix: -1.69 (0.86), residues: 28 sheet: 0.41 (0.36), residues: 239 loop : -0.68 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.027 0.002 TYR L 51 PHE 0.009 0.001 PHE H 177 TRP 0.016 0.001 TRP H 47 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.24 ( 4740) covalent geometry : angle 0.66760 / 0.38 ( 6473) SS BOND : bond 0.00262 / 0.11 ( 7) SS BOND : angle 0.81841 / 0.47 ( 16) hydrogen bonds : bond 0.25951 / 17.85 ( 154) hydrogen bonds : angle 10.73544 / 7.62 ( 437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.158 Fit side-chains REVERT: H 54 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8848 (tt) REVERT: H 111 MET cc_start: 0.7896 (mpp) cc_final: 0.7416 (mtm) REVERT: A 349 ILE cc_start: 0.8873 (mm) cc_final: 0.8398 (mt) REVERT: A 466 SER cc_start: 0.7750 (p) cc_final: 0.7510 (t) REVERT: A 492 ASN cc_start: 0.7475 (m110) cc_final: 0.7213 (p0) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.0769 time to fit residues: 9.9794 Evaluate side-chains 61 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.190011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118366 restraints weight = 5528.669| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.18 r_work: 0.3098 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4747 Z= 0.138 Angle : 0.588 7.453 6489 Z= 0.303 Chirality : 0.044 0.136 734 Planarity : 0.004 0.032 831 Dihedral : 4.183 41.423 667 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.12 % Allowed : 23.08 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.35), residues: 608 helix: -1.78 (0.76), residues: 44 sheet: 0.59 (0.35), residues: 241 loop : -0.35 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.019 0.001 TYR A 468 PHE 0.014 0.002 PHE H 133 TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4740) covalent geometry : angle 0.58695 / 0.30 ( 6473) SS BOND : bond 0.00575 / 0.45 ( 7) SS BOND : angle 0.83288 / 0.47 ( 16) hydrogen bonds : bond 0.04466 / 3.06 ( 154) hydrogen bonds : angle 6.95950 / 4.93 ( 437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.165 Fit side-chains REVERT: H 48 MET cc_start: 0.8850 (mtm) cc_final: 0.8576 (mtm) REVERT: H 69 MET cc_start: 0.8262 (tpt) cc_final: 0.7900 (mmm) REVERT: H 133 PHE cc_start: 0.7063 (m-80) cc_final: 0.6710 (m-80) REVERT: H 156 TYR cc_start: 0.7045 (p90) cc_final: 0.6745 (p90) REVERT: H 175 HIS cc_start: 0.6164 (t-90) cc_final: 0.5492 (t-90) REVERT: H 211 HIS cc_start: 0.8360 (t-90) cc_final: 0.8056 (t-90) REVERT: L 64 PHE cc_start: 0.7571 (m-80) cc_final: 0.7204 (m-80) REVERT: L 183 LEU cc_start: 0.8983 (tp) cc_final: 0.8554 (mm) REVERT: A 492 ASN cc_start: 0.8401 (m110) cc_final: 0.7377 (p0) outliers start: 11 outliers final: 5 residues processed: 82 average time/residue: 0.0544 time to fit residues: 6.0658 Evaluate side-chains 66 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 175 ASN Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 467 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 19 optimal weight: 50.0000 chunk 21 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 39 GLN L 40 GLN L 81 GLN A 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.187848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135173 restraints weight = 5415.960| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.06 r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 4747 Z= 0.352 Angle : 0.713 6.188 6489 Z= 0.368 Chirality : 0.048 0.141 734 Planarity : 0.005 0.049 831 Dihedral : 4.525 20.267 665 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.62 % Allowed : 21.15 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.35), residues: 608 helix: -1.81 (0.75), residues: 44 sheet: 0.29 (0.34), residues: 248 loop : -0.47 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 452 TYR 0.029 0.003 TYR A 468 PHE 0.021 0.002 PHE A 420 TRP 0.015 0.002 TRP A 427 HIS 0.005 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.35 ( 4740) covalent geometry : angle 0.71085 / 0.37 ( 6473) SS BOND : bond 0.00409 / 0.24 ( 7) SS BOND : angle 1.30295 / 0.77 ( 16) hydrogen bonds : bond 0.04795 / 3.27 ( 154) hydrogen bonds : angle 6.77249 / 4.75 ( 437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 69 MET cc_start: 0.8454 (tpt) cc_final: 0.8163 (mmm) REVERT: H 111 MET cc_start: 0.8422 (mtm) cc_final: 0.8029 (mtt) REVERT: H 133 PHE cc_start: 0.6943 (m-80) cc_final: 0.6339 (m-80) REVERT: H 175 HIS cc_start: 0.6823 (t-90) cc_final: 0.6040 (t-90) REVERT: H 189 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8341 (pp) REVERT: L 123 PHE cc_start: 0.6688 (m-80) cc_final: 0.6305 (m-10) REVERT: L 134 LYS cc_start: 0.7302 (tppt) cc_final: 0.6833 (pttt) REVERT: L 196 TYR cc_start: 0.7071 (m-80) cc_final: 0.6727 (m-80) REVERT: A 442 HIS cc_start: 0.8503 (t70) cc_final: 0.8260 (t-90) outliers start: 24 outliers final: 15 residues processed: 89 average time/residue: 0.0649 time to fit residues: 7.5310 Evaluate side-chains 80 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115897 restraints weight = 5323.065| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.35 r_work: 0.3138 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4747 Z= 0.119 Angle : 0.579 10.113 6489 Z= 0.287 Chirality : 0.044 0.126 734 Planarity : 0.004 0.029 831 Dihedral : 4.080 17.936 665 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.50 % Allowed : 22.69 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.35), residues: 608 helix: -1.67 (0.78), residues: 44 sheet: 0.34 (0.35), residues: 236 loop : -0.40 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.024 0.001 TYR A 468 PHE 0.013 0.001 PHE L 64 TRP 0.009 0.001 TRP A 427 HIS 0.005 0.001 HIS H 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4740) covalent geometry : angle 0.57844 / 0.29 ( 6473) SS BOND : bond 0.00160 / 0.11 ( 7) SS BOND : angle 0.78916 / 0.43 ( 16) hydrogen bonds : bond 0.03318 / 2.24 ( 154) hydrogen bonds : angle 6.09413 / 4.26 ( 437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8383 (tpt) cc_final: 0.8128 (mmm) REVERT: H 111 MET cc_start: 0.8272 (mtm) cc_final: 0.8022 (mtt) REVERT: H 133 PHE cc_start: 0.6962 (m-80) cc_final: 0.6620 (m-80) REVERT: H 175 HIS cc_start: 0.6760 (t-90) cc_final: 0.6099 (t-90) REVERT: H 189 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8335 (pp) REVERT: L 81 GLN cc_start: 0.8036 (mp10) cc_final: 0.7818 (mp10) REVERT: L 171 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8216 (mmtt) REVERT: L 183 LEU cc_start: 0.9000 (tp) cc_final: 0.8745 (mt) REVERT: L 196 TYR cc_start: 0.7330 (m-80) cc_final: 0.6842 (m-80) REVERT: A 379 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8609 (mt) REVERT: A 442 HIS cc_start: 0.8522 (t70) cc_final: 0.8236 (t-90) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.0587 time to fit residues: 5.9729 Evaluate side-chains 68 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.191657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123304 restraints weight = 5425.804| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.00 r_work: 0.3018 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4747 Z= 0.135 Angle : 0.576 9.275 6489 Z= 0.286 Chirality : 0.044 0.126 734 Planarity : 0.004 0.027 831 Dihedral : 3.959 17.247 665 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.50 % Allowed : 23.27 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.35), residues: 608 helix: -1.61 (0.78), residues: 44 sheet: 0.26 (0.35), residues: 236 loop : -0.40 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.020 0.001 TYR A 468 PHE 0.015 0.001 PHE L 64 TRP 0.010 0.001 TRP A 427 HIS 0.001 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4740) covalent geometry : angle 0.57494 / 0.29 ( 6473) SS BOND : bond 0.00297 / 0.24 ( 7) SS BOND : angle 0.77751 / 0.45 ( 16) hydrogen bonds : bond 0.03279 / 2.20 ( 154) hydrogen bonds : angle 5.77391 / 4.02 ( 437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8350 (tpt) cc_final: 0.8091 (mmm) REVERT: H 111 MET cc_start: 0.8333 (mtm) cc_final: 0.8021 (mtt) REVERT: H 133 PHE cc_start: 0.7071 (m-80) cc_final: 0.6452 (m-80) REVERT: H 189 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8335 (pp) REVERT: L 81 GLN cc_start: 0.8204 (mp10) cc_final: 0.7666 (mp10) REVERT: L 134 LYS cc_start: 0.7286 (tppt) cc_final: 0.6995 (pttt) REVERT: L 183 LEU cc_start: 0.9038 (tp) cc_final: 0.8782 (mt) REVERT: L 196 TYR cc_start: 0.7290 (m-80) cc_final: 0.6866 (m-80) REVERT: A 379 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 442 HIS cc_start: 0.8580 (t70) cc_final: 0.8305 (t-90) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.0617 time to fit residues: 6.0204 Evaluate side-chains 71 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.191491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115500 restraints weight = 5402.000| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.39 r_work: 0.3043 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4747 Z= 0.137 Angle : 0.561 8.790 6489 Z= 0.280 Chirality : 0.043 0.124 734 Planarity : 0.003 0.026 831 Dihedral : 3.938 17.280 665 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.88 % Allowed : 23.08 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.35), residues: 608 helix: -1.52 (0.78), residues: 44 sheet: 0.18 (0.34), residues: 238 loop : -0.38 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.019 0.001 TYR A 468 PHE 0.011 0.001 PHE L 64 TRP 0.009 0.001 TRP A 427 HIS 0.001 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4740) covalent geometry : angle 0.56070 / 0.28 ( 6473) SS BOND : bond 0.00128 / 0.09 ( 7) SS BOND : angle 0.80792 / 0.45 ( 16) hydrogen bonds : bond 0.03215 / 2.15 ( 154) hydrogen bonds : angle 5.60922 / 3.91 ( 437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: H 20 VAL cc_start: 0.9050 (t) cc_final: 0.8711 (m) REVERT: H 69 MET cc_start: 0.8231 (tpt) cc_final: 0.7963 (mmm) REVERT: H 189 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8318 (pp) REVERT: L 81 GLN cc_start: 0.8231 (mp10) cc_final: 0.7386 (mp10) REVERT: L 134 LYS cc_start: 0.7414 (tppt) cc_final: 0.7040 (pttt) REVERT: L 171 LYS cc_start: 0.8326 (mmmm) cc_final: 0.8068 (mmmm) REVERT: L 183 LEU cc_start: 0.9031 (tp) cc_final: 0.8771 (mt) REVERT: L 196 TYR cc_start: 0.7307 (m-80) cc_final: 0.6879 (m-80) REVERT: A 379 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8593 (mt) REVERT: A 397 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7482 (mp0) REVERT: A 442 HIS cc_start: 0.8497 (t70) cc_final: 0.8187 (t-90) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.0579 time to fit residues: 6.0286 Evaluate side-chains 77 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.190041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142254 restraints weight = 5347.732| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.91 r_work: 0.3239 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4747 Z= 0.178 Angle : 0.585 8.252 6489 Z= 0.293 Chirality : 0.044 0.128 734 Planarity : 0.004 0.026 831 Dihedral : 4.010 19.397 665 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 23.08 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.35), residues: 608 helix: -1.52 (0.76), residues: 44 sheet: 0.18 (0.34), residues: 238 loop : -0.40 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.026 0.002 TYR A 468 PHE 0.011 0.001 PHE L 64 TRP 0.009 0.001 TRP A 427 HIS 0.001 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 4740) covalent geometry : angle 0.58400 / 0.29 ( 6473) SS BOND : bond 0.00100 / 0.05 ( 7) SS BOND : angle 0.92764 / 0.53 ( 16) hydrogen bonds : bond 0.03449 / 2.33 ( 154) hydrogen bonds : angle 5.64213 / 3.93 ( 437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: H 20 VAL cc_start: 0.9036 (t) cc_final: 0.8695 (m) REVERT: H 69 MET cc_start: 0.8337 (tpt) cc_final: 0.8121 (mmm) REVERT: H 189 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8426 (pp) REVERT: L 81 GLN cc_start: 0.8170 (mp10) cc_final: 0.7535 (mp10) REVERT: L 85 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7333 (tm-30) REVERT: L 134 LYS cc_start: 0.7759 (tppt) cc_final: 0.7378 (pttt) REVERT: L 171 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7705 (mmmm) REVERT: L 183 LEU cc_start: 0.8931 (tp) cc_final: 0.8723 (mt) REVERT: L 196 TYR cc_start: 0.7280 (m-80) cc_final: 0.6964 (m-80) REVERT: A 379 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 442 HIS cc_start: 0.8371 (t70) cc_final: 0.8110 (t-90) outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 0.0701 time to fit residues: 7.2377 Evaluate side-chains 80 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.190536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136949 restraints weight = 5474.302| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.95 r_work: 0.3220 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4747 Z= 0.157 Angle : 0.574 8.208 6489 Z= 0.286 Chirality : 0.044 0.124 734 Planarity : 0.004 0.026 831 Dihedral : 3.971 19.414 665 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.69 % Allowed : 22.88 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.35), residues: 608 helix: -1.45 (0.75), residues: 44 sheet: 0.25 (0.34), residues: 236 loop : -0.39 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 394 TYR 0.028 0.002 TYR A 468 PHE 0.010 0.001 PHE L 64 TRP 0.009 0.001 TRP A 427 HIS 0.001 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4740) covalent geometry : angle 0.57318 / 0.29 ( 6473) SS BOND : bond 0.00099 / 0.06 ( 7) SS BOND : angle 0.86204 / 0.48 ( 16) hydrogen bonds : bond 0.03268 / 2.18 ( 154) hydrogen bonds : angle 5.54673 / 3.86 ( 437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: H 20 VAL cc_start: 0.9041 (t) cc_final: 0.8720 (m) REVERT: H 69 MET cc_start: 0.8447 (tpt) cc_final: 0.8221 (mmm) REVERT: H 133 PHE cc_start: 0.6868 (m-80) cc_final: 0.6642 (m-80) REVERT: H 189 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8442 (pp) REVERT: L 81 GLN cc_start: 0.8072 (mp10) cc_final: 0.7424 (mp10) REVERT: L 85 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7315 (tm-30) REVERT: L 134 LYS cc_start: 0.7750 (tppt) cc_final: 0.7500 (pttt) REVERT: L 171 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8024 (mmmm) REVERT: L 176 LYS cc_start: 0.7294 (mmmm) cc_final: 0.6753 (mmmm) REVERT: L 183 LEU cc_start: 0.8849 (tp) cc_final: 0.8629 (mt) REVERT: L 196 TYR cc_start: 0.7140 (m-80) cc_final: 0.6869 (m-80) REVERT: A 379 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8627 (mt) REVERT: A 397 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7316 (mp0) REVERT: A 442 HIS cc_start: 0.8433 (t70) cc_final: 0.8187 (t-90) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.0674 time to fit residues: 7.0754 Evaluate side-chains 83 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.190038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121914 restraints weight = 5348.275| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.37 r_work: 0.3077 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4747 Z= 0.172 Angle : 0.582 8.092 6489 Z= 0.292 Chirality : 0.044 0.125 734 Planarity : 0.004 0.026 831 Dihedral : 4.013 20.293 665 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.46 % Allowed : 22.31 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.35), residues: 608 helix: -1.49 (0.74), residues: 44 sheet: 0.29 (0.34), residues: 246 loop : -0.43 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.030 0.002 TYR A 468 PHE 0.009 0.001 PHE L 64 TRP 0.009 0.001 TRP A 427 HIS 0.001 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 4740) covalent geometry : angle 0.58097 / 0.29 ( 6473) SS BOND : bond 0.00107 / 0.06 ( 7) SS BOND : angle 0.92859 / 0.53 ( 16) hydrogen bonds : bond 0.03378 / 2.27 ( 154) hydrogen bonds : angle 5.54504 / 3.86 ( 437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: H 20 VAL cc_start: 0.9072 (t) cc_final: 0.8705 (m) REVERT: L 81 GLN cc_start: 0.7959 (mp10) cc_final: 0.7244 (mp10) REVERT: L 134 LYS cc_start: 0.7915 (tppt) cc_final: 0.7700 (pttt) REVERT: L 171 LYS cc_start: 0.8468 (mmmm) cc_final: 0.7985 (mmmm) REVERT: L 176 LYS cc_start: 0.7191 (mmmm) cc_final: 0.6940 (mmmm) REVERT: L 183 LEU cc_start: 0.8980 (tp) cc_final: 0.8681 (mt) REVERT: L 196 TYR cc_start: 0.7474 (m-80) cc_final: 0.7046 (m-80) REVERT: A 379 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 397 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7521 (mp0) REVERT: A 442 HIS cc_start: 0.8626 (t70) cc_final: 0.8373 (t-90) outliers start: 18 outliers final: 15 residues processed: 84 average time/residue: 0.0639 time to fit residues: 6.9640 Evaluate side-chains 85 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.3662 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.192882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123838 restraints weight = 5391.949| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.11 r_work: 0.3105 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4747 Z= 0.101 Angle : 0.552 8.558 6489 Z= 0.275 Chirality : 0.043 0.125 734 Planarity : 0.003 0.026 831 Dihedral : 3.790 18.133 665 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.69 % Allowed : 23.27 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.35), residues: 608 helix: -1.76 (0.66), residues: 50 sheet: 0.37 (0.34), residues: 236 loop : -0.31 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.030 0.001 TYR A 468 PHE 0.009 0.001 PHE L 64 TRP 0.015 0.001 TRP H 47 HIS 0.001 0.000 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 4740) covalent geometry : angle 0.55146 / 0.27 ( 6473) SS BOND : bond 0.00198 / 0.15 ( 7) SS BOND : angle 0.79378 / 0.44 ( 16) hydrogen bonds : bond 0.02867 / 1.90 ( 154) hydrogen bonds : angle 5.24650 / 3.66 ( 437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: H 20 VAL cc_start: 0.9053 (t) cc_final: 0.8671 (m) REVERT: H 69 MET cc_start: 0.8319 (tpt) cc_final: 0.8095 (mmm) REVERT: H 85 SER cc_start: 0.8647 (t) cc_final: 0.8037 (p) REVERT: H 157 PHE cc_start: 0.8007 (t80) cc_final: 0.7687 (t80) REVERT: L 81 GLN cc_start: 0.7946 (mp10) cc_final: 0.7160 (mp10) REVERT: L 171 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8123 (tptt) REVERT: L 183 LEU cc_start: 0.8935 (tp) cc_final: 0.8621 (mt) REVERT: L 196 TYR cc_start: 0.7419 (m-80) cc_final: 0.7036 (m-80) REVERT: A 397 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7533 (mp0) REVERT: A 436 ASN cc_start: 0.8098 (p0) cc_final: 0.7842 (p0) REVERT: A 442 HIS cc_start: 0.8574 (t70) cc_final: 0.8312 (t-90) outliers start: 14 outliers final: 14 residues processed: 83 average time/residue: 0.0661 time to fit residues: 7.0485 Evaluate side-chains 84 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137380 restraints weight = 5404.373| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.96 r_work: 0.3205 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4747 Z= 0.188 Angle : 0.593 7.597 6489 Z= 0.296 Chirality : 0.044 0.126 734 Planarity : 0.004 0.024 831 Dihedral : 3.984 19.863 665 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.69 % Allowed : 23.85 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.35), residues: 608 helix: -1.42 (0.73), residues: 44 sheet: 0.38 (0.34), residues: 246 loop : -0.39 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.029 0.002 TYR A 468 PHE 0.010 0.002 PHE A 391 TRP 0.010 0.001 TRP A 427 HIS 0.001 0.000 HIS H 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 4740) covalent geometry : angle 0.59180 / 0.30 ( 6473) SS BOND : bond 0.00118 / 0.06 ( 7) SS BOND : angle 0.97455 / 0.57 ( 16) hydrogen bonds : bond 0.03463 / 2.30 ( 154) hydrogen bonds : angle 5.41720 / 3.76 ( 437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.26 seconds wall clock time: 28 minutes 22.06 seconds (1702.06 seconds total)