Starting phenix.real_space_refine on Wed Mar 4 10:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uml_26603/03_2026/7uml_26603.map" } resolution = 3.5 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= 0.053 sd= 1.358 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 37 5.16 5 C 4272 2.51 5 N 1126 2.21 5 O 1302 1.98 5 H 6477 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5980 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2741 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 551 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 531 Classifications: {'peptide': 39} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "F" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 391 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 2.40, per 1000 atoms: 0.18 Number of scatterers: 13227 At special positions: 0 Unit cell: (143.65, 100.3, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 13 15.00 O 1302 8.00 N 1126 7.00 C 4272 6.00 H 6477 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.12 Conformation dependent library (CDL) restraints added in 471.7 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 38.2% alpha, 13.5% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.732A pdb=" N PHE A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.636A pdb=" N LYS A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.539A pdb=" N VAL A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.075A pdb=" N THR A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.623A pdb=" N ILE A 218 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 220 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.412A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.718A pdb=" N ASN B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.755A pdb=" N LEU B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.571A pdb=" N PHE B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.733A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.593A pdb=" N LEU C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.550A pdb=" N HIS C 192 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 193 " --> pdb=" O TRP C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'D' and resid 27 through 35 removed outlier: 4.510A pdb=" N TYR D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.420A pdb=" N LEU A 40 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 213 removed outlier: 6.959A pdb=" N ILE B 211 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 143 Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.578A pdb=" N ILE D 14 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 5 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS E 349 " --> pdb=" O LYS D 6 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6470 1.03 - 1.23: 22 1.23 - 1.42: 3001 1.42 - 1.62: 3863 1.62 - 1.81: 67 Bond restraints: 13423 Sorted by residual: bond pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.46e+00 bond pdb=" N GLY C 146 " pdb=" CA GLY C 146 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.88e-01 bond pdb=" CA PHE A 182 " pdb=" CB PHE A 182 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.66e-02 3.63e+03 6.66e-01 bond pdb=" C ASN B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 1.331 1.348 -0.017 2.07e-02 2.33e+03 6.56e-01 bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.44e-01 ... (remaining 13418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 23603 1.51 - 3.02: 543 3.02 - 4.53: 50 4.53 - 6.04: 7 6.04 - 7.55: 2 Bond angle restraints: 24205 Sorted by residual: angle pdb=" C SER C 224 " pdb=" N ILE C 225 " pdb=" CA ILE C 225 " ideal model delta sigma weight residual 121.97 129.52 -7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" N ILE C 225 " pdb=" CA ILE C 225 " pdb=" C ILE C 225 " ideal model delta sigma weight residual 109.34 102.84 6.50 2.08e+00 2.31e-01 9.78e+00 angle pdb=" C ASP A 85 " pdb=" N LYS A 86 " pdb=" CA LYS A 86 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C LYS B 197 " pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.37e+00 angle pdb=" N PHE B 198 " pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 110.49 115.35 -4.86 1.69e+00 3.50e-01 8.27e+00 ... (remaining 24200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 6170 34.69 - 69.38: 237 69.38 - 104.07: 6 104.07 - 138.76: 1 138.76 - 173.45: 1 Dihedral angle restraints: 6415 sinusoidal: 3523 harmonic: 2892 Sorted by residual: dihedral pdb=" CA ILE C 225 " pdb=" C ILE C 225 " pdb=" N SER C 226 " pdb=" CA SER C 226 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" O4' U R 36 " pdb=" C1' U R 36 " pdb=" N1 U R 36 " pdb=" C2 U R 36 " ideal model delta sinusoidal sigma weight residual -160.00 13.45 -173.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U R 27 " pdb=" C1' U R 27 " pdb=" N1 U R 27 " pdb=" C2 U R 27 " ideal model delta sinusoidal sigma weight residual -160.00 -26.98 -133.02 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 6412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 703 0.034 - 0.068: 223 0.068 - 0.102: 57 0.102 - 0.135: 26 0.135 - 0.169: 6 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C1' U R 36 " pdb=" O4' U R 36 " pdb=" C2' U R 36 " pdb=" N1 U R 36 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE C 225 " pdb=" N ILE C 225 " pdb=" C ILE C 225 " pdb=" CB ILE C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 68 " pdb=" N VAL B 68 " pdb=" C VAL B 68 " pdb=" CB VAL B 68 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1012 not shown) Planarity restraints: 1933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 197 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS B 197 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 197 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 128 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO C 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 160 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 161 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.026 5.00e-02 4.00e+02 ... (remaining 1930 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1020 2.21 - 2.81: 26688 2.81 - 3.41: 33005 3.41 - 4.00: 42734 4.00 - 4.60: 65211 Nonbonded interactions: 168658 Sorted by model distance: nonbonded pdb=" HE1 TRP B 190 " pdb=" O TRP B 220 " model vdw 1.616 2.450 nonbonded pdb=" HH TYR A 152 " pdb=" OP2 U R 35 " model vdw 1.618 2.450 nonbonded pdb=" H SER A 291 " pdb=" OP2 U R 31 " model vdw 1.644 2.450 nonbonded pdb=" O ARG D 7 " pdb=" H ASN D 11 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLN E 346 " pdb=" H TYR E 355 " model vdw 1.682 2.450 ... (remaining 168653 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 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 59 through 227)) selection = (chain 'C' and resid 58 through 227) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6946 Z= 0.116 Angle : 0.579 7.548 9448 Z= 0.314 Chirality : 0.040 0.169 1015 Planarity : 0.005 0.051 1173 Dihedral : 16.391 173.453 2661 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.01 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.22 % Twisted General : 0.26 % 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: -2.75 (0.27), residues: 798 helix: -0.80 (0.30), residues: 273 sheet: -0.74 (0.49), residues: 99 loop : -2.91 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.014 0.001 TYR B 178 PHE 0.013 0.001 PHE C 208 TRP 0.030 0.001 TRP A 88 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6946) covalent geometry : angle 0.57850 ( 9448) hydrogen bonds : bond 0.16876 ( 247) hydrogen bonds : angle 6.84100 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.7194 (m-10) cc_final: 0.6984 (m-10) REVERT: C 188 MET cc_start: 0.6581 (mmp) cc_final: 0.6269 (mmt) REVERT: D 4 THR cc_start: 0.8169 (p) cc_final: 0.7964 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1919 time to fit residues: 44.2100 Evaluate side-chains 132 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.196084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170855 restraints weight = 30884.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175577 restraints weight = 13548.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178505 restraints weight = 7726.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.180427 restraints weight = 5267.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181749 restraints weight = 4016.786| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.146 Angle : 0.569 4.801 9448 Z= 0.303 Chirality : 0.040 0.158 1015 Planarity : 0.005 0.040 1173 Dihedral : 14.871 172.282 1096 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.14 % Favored : 92.23 % Rotamer: Outliers : 1.73 % Allowed : 8.63 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.20 (0.28), residues: 798 helix: -0.13 (0.31), residues: 278 sheet: -0.50 (0.47), residues: 109 loop : -2.81 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.010 0.001 TYR C 178 PHE 0.014 0.001 PHE B 198 TRP 0.004 0.001 TRP A 88 HIS 0.003 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6946) covalent geometry : angle 0.56909 ( 9448) hydrogen bonds : bond 0.04634 ( 247) hydrogen bonds : angle 5.37324 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.6630 (p0) cc_final: 0.6140 (p0) REVERT: B 92 ASP cc_start: 0.8046 (p0) cc_final: 0.7768 (p0) REVERT: C 175 MET cc_start: 0.4106 (mtt) cc_final: 0.3853 (mtt) REVERT: C 188 MET cc_start: 0.6953 (mmp) cc_final: 0.6529 (mmt) REVERT: D 4 THR cc_start: 0.8355 (p) cc_final: 0.8117 (t) outliers start: 12 outliers final: 11 residues processed: 149 average time/residue: 0.1754 time to fit residues: 34.3048 Evaluate side-chains 144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165809 restraints weight = 31452.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170567 restraints weight = 14262.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.173602 restraints weight = 8394.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175427 restraints weight = 5807.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176361 restraints weight = 4532.589| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6946 Z= 0.154 Angle : 0.566 4.875 9448 Z= 0.301 Chirality : 0.040 0.171 1015 Planarity : 0.005 0.037 1173 Dihedral : 14.678 172.810 1096 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.02 % Favored : 91.60 % Rotamer: Outliers : 2.45 % Allowed : 11.22 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.28), residues: 798 helix: 0.04 (0.31), residues: 281 sheet: -0.71 (0.45), residues: 119 loop : -2.74 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.011 0.001 TYR B 140 PHE 0.015 0.001 PHE A 205 TRP 0.005 0.001 TRP A 248 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6946) covalent geometry : angle 0.56579 ( 9448) hydrogen bonds : bond 0.04364 ( 247) hydrogen bonds : angle 5.17359 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8056 (p0) cc_final: 0.7745 (p0) REVERT: C 188 MET cc_start: 0.7054 (mmp) cc_final: 0.6553 (mmt) REVERT: D 4 THR cc_start: 0.8345 (p) cc_final: 0.8100 (t) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 0.1775 time to fit residues: 32.3224 Evaluate side-chains 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163610 restraints weight = 31590.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168166 restraints weight = 15070.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.170948 restraints weight = 9049.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172847 restraints weight = 6504.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173770 restraints weight = 5151.701| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6946 Z= 0.178 Angle : 0.573 4.508 9448 Z= 0.306 Chirality : 0.040 0.180 1015 Planarity : 0.005 0.037 1173 Dihedral : 14.548 172.619 1096 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.90 % Favored : 89.60 % Rotamer: Outliers : 3.17 % Allowed : 13.53 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.28), residues: 798 helix: 0.03 (0.32), residues: 281 sheet: -0.81 (0.46), residues: 119 loop : -2.71 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.012 0.001 TYR A 277 PHE 0.015 0.001 PHE B 110 TRP 0.007 0.001 TRP A 248 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6946) covalent geometry : angle 0.57323 ( 9448) hydrogen bonds : bond 0.04295 ( 247) hydrogen bonds : angle 5.14070 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8041 (p0) cc_final: 0.7708 (p0) REVERT: C 188 MET cc_start: 0.6988 (mmp) cc_final: 0.6406 (mmt) REVERT: D 4 THR cc_start: 0.8349 (p) cc_final: 0.8105 (t) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.1691 time to fit residues: 31.1406 Evaluate side-chains 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.192150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165571 restraints weight = 31663.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170077 restraints weight = 14957.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.172921 restraints weight = 9005.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174718 restraints weight = 6386.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176036 restraints weight = 5083.485| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6946 Z= 0.143 Angle : 0.550 4.558 9448 Z= 0.292 Chirality : 0.039 0.183 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.466 173.617 1096 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.90 % Favored : 90.60 % Rotamer: Outliers : 2.88 % Allowed : 14.96 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.98 (0.29), residues: 798 helix: 0.04 (0.31), residues: 287 sheet: -0.75 (0.47), residues: 119 loop : -2.63 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.011 0.001 TYR B 140 PHE 0.014 0.001 PHE B 110 TRP 0.005 0.001 TRP A 248 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6946) covalent geometry : angle 0.55043 ( 9448) hydrogen bonds : bond 0.03904 ( 247) hydrogen bonds : angle 4.97841 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6503 (tmm) REVERT: B 92 ASP cc_start: 0.8012 (p0) cc_final: 0.7683 (p0) REVERT: C 188 MET cc_start: 0.6918 (mmp) cc_final: 0.6293 (mmt) REVERT: D 4 THR cc_start: 0.8285 (p) cc_final: 0.8059 (t) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.1709 time to fit residues: 31.9223 Evaluate side-chains 145 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161415 restraints weight = 31781.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.166054 restraints weight = 14788.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168945 restraints weight = 8741.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170642 restraints weight = 6217.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.171974 restraints weight = 4935.870| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6946 Z= 0.212 Angle : 0.603 4.777 9448 Z= 0.322 Chirality : 0.041 0.182 1015 Planarity : 0.005 0.039 1173 Dihedral : 14.509 171.863 1096 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.15 % Favored : 88.22 % Rotamer: Outliers : 3.02 % Allowed : 15.97 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.02 (0.28), residues: 798 helix: 0.01 (0.31), residues: 281 sheet: -0.54 (0.49), residues: 111 loop : -2.67 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.015 0.002 TYR B 140 PHE 0.012 0.002 PHE B 110 TRP 0.008 0.001 TRP A 248 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 6946) covalent geometry : angle 0.60311 ( 9448) hydrogen bonds : bond 0.04518 ( 247) hydrogen bonds : angle 5.24217 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8161 (p0) cc_final: 0.7833 (p0) REVERT: C 188 MET cc_start: 0.6995 (mmp) cc_final: 0.6364 (mmt) REVERT: D 4 THR cc_start: 0.8344 (p) cc_final: 0.8070 (t) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.1675 time to fit residues: 30.6030 Evaluate side-chains 145 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.192322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166173 restraints weight = 31140.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.170688 restraints weight = 14608.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.173569 restraints weight = 8684.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175139 restraints weight = 6159.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176515 restraints weight = 4950.152| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.116 Angle : 0.536 4.446 9448 Z= 0.283 Chirality : 0.039 0.186 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.383 174.968 1096 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.40 % Favored : 90.98 % Rotamer: Outliers : 2.59 % Allowed : 17.27 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.76 (0.29), residues: 798 helix: 0.33 (0.32), residues: 282 sheet: -0.86 (0.47), residues: 119 loop : -2.48 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.012 0.001 TYR A 277 PHE 0.010 0.001 PHE B 110 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6946) covalent geometry : angle 0.53611 ( 9448) hydrogen bonds : bond 0.03576 ( 247) hydrogen bonds : angle 4.76876 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7998 (p0) cc_final: 0.7650 (p0) REVERT: C 188 MET cc_start: 0.6882 (mmp) cc_final: 0.6318 (mmt) REVERT: D 4 THR cc_start: 0.8299 (p) cc_final: 0.8062 (t) outliers start: 18 outliers final: 17 residues processed: 139 average time/residue: 0.1578 time to fit residues: 29.8101 Evaluate side-chains 146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.189374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162790 restraints weight = 31478.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167380 restraints weight = 14518.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170268 restraints weight = 8632.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172225 restraints weight = 6066.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173216 restraints weight = 4748.189| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6946 Z= 0.171 Angle : 0.568 4.558 9448 Z= 0.302 Chirality : 0.040 0.177 1015 Planarity : 0.005 0.037 1173 Dihedral : 14.409 171.782 1096 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.28 % Favored : 88.10 % Rotamer: Outliers : 2.88 % Allowed : 17.70 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.77 (0.29), residues: 798 helix: 0.29 (0.32), residues: 282 sheet: -0.52 (0.49), residues: 111 loop : -2.55 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.013 0.001 TYR A 277 PHE 0.009 0.001 PHE A 281 TRP 0.006 0.001 TRP A 248 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6946) covalent geometry : angle 0.56781 ( 9448) hydrogen bonds : bond 0.04063 ( 247) hydrogen bonds : angle 4.95406 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8115 (p0) cc_final: 0.7761 (p0) REVERT: C 188 MET cc_start: 0.6905 (mmp) cc_final: 0.6321 (mmt) REVERT: D 4 THR cc_start: 0.8332 (p) cc_final: 0.8081 (t) outliers start: 20 outliers final: 18 residues processed: 133 average time/residue: 0.1556 time to fit residues: 28.0729 Evaluate side-chains 142 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166158 restraints weight = 31510.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170829 restraints weight = 14148.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173727 restraints weight = 8302.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175696 restraints weight = 5777.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.177062 restraints weight = 4454.575| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6946 Z= 0.105 Angle : 0.525 4.808 9448 Z= 0.276 Chirality : 0.039 0.180 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.314 174.489 1096 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.15 % Favored : 91.23 % Rotamer: Outliers : 2.16 % Allowed : 18.13 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.52 (0.30), residues: 798 helix: 0.53 (0.32), residues: 284 sheet: -0.80 (0.47), residues: 119 loop : -2.33 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.013 0.001 TYR A 277 PHE 0.010 0.001 PHE B 110 TRP 0.006 0.001 TRP C 190 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6946) covalent geometry : angle 0.52461 ( 9448) hydrogen bonds : bond 0.03321 ( 247) hydrogen bonds : angle 4.60567 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.7351 (tmm) cc_final: 0.6680 (tmm) REVERT: B 92 ASP cc_start: 0.8046 (p0) cc_final: 0.7687 (p0) REVERT: C 188 MET cc_start: 0.6868 (mmp) cc_final: 0.6306 (mmt) REVERT: D 4 THR cc_start: 0.8350 (p) cc_final: 0.8134 (t) outliers start: 15 outliers final: 14 residues processed: 137 average time/residue: 0.1542 time to fit residues: 28.9458 Evaluate side-chains 140 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166106 restraints weight = 31314.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170752 restraints weight = 14047.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173648 restraints weight = 8180.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175592 restraints weight = 5706.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176522 restraints weight = 4442.540| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6946 Z= 0.110 Angle : 0.528 4.807 9448 Z= 0.276 Chirality : 0.039 0.170 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.305 172.919 1096 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.52 % Favored : 89.97 % Rotamer: Outliers : 2.16 % Allowed : 18.27 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.34 (0.30), residues: 798 helix: 0.63 (0.32), residues: 286 sheet: -0.35 (0.50), residues: 109 loop : -2.28 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.012 0.001 TYR A 277 PHE 0.011 0.001 PHE B 110 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6946) covalent geometry : angle 0.52778 ( 9448) hydrogen bonds : bond 0.03329 ( 247) hydrogen bonds : angle 4.52810 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.7379 (tmm) cc_final: 0.6645 (tmm) REVERT: B 92 ASP cc_start: 0.7989 (p0) cc_final: 0.7653 (p0) REVERT: C 188 MET cc_start: 0.6908 (mmp) cc_final: 0.6405 (mmt) REVERT: D 4 THR cc_start: 0.8369 (p) cc_final: 0.8166 (t) outliers start: 15 outliers final: 14 residues processed: 139 average time/residue: 0.1623 time to fit residues: 30.5746 Evaluate side-chains 142 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 62 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.190826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.164613 restraints weight = 31392.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169274 restraints weight = 14165.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172180 restraints weight = 8307.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174118 restraints weight = 5815.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175001 restraints weight = 4549.808| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.131 Angle : 0.543 4.798 9448 Z= 0.283 Chirality : 0.039 0.164 1015 Planarity : 0.005 0.094 1173 Dihedral : 14.304 172.309 1096 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.15 % Favored : 89.35 % Rotamer: Outliers : 2.30 % Allowed : 18.42 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.40 (0.30), residues: 798 helix: 0.61 (0.32), residues: 285 sheet: -0.36 (0.50), residues: 109 loop : -2.33 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.013 0.001 TYR A 277 PHE 0.014 0.001 PHE B 110 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6946) covalent geometry : angle 0.54323 ( 9448) hydrogen bonds : bond 0.03500 ( 247) hydrogen bonds : angle 4.60923 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.62 seconds wall clock time: 43 minutes 13.52 seconds (2593.52 seconds total)