Starting phenix.real_space_refine on Fri Jul 3 08:03:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uml_26603/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.map" model { file = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2026/7uml_26603.cif" } 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-6108/lib/python3.11/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: 2.01, per 1000 atoms: 0.15 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: 0.85 Conformation dependent library (CDL) restraints added in 426.4 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: 1.85 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: 2.19 Time building geometry restraints manager: 1.23 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: 6148 34.69 - 69.38: 194 69.38 - 104.07: 6 104.07 - 138.76: 1 138.76 - 173.45: 1 Dihedral angle restraints: 6350 sinusoidal: 3458 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 6347 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 15.494 173.453 2609 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/Z covalent geometry : bond 0.00254 / 0.12 ( 6946) covalent geometry : angle 0.57850 / 0.31 ( 9448) hydrogen bonds : bond 0.16876 / 10.34 ( 247) hydrogen bonds : angle 6.84100 / 4.68 ( 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 : 0.340 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: 0.1694 time to fit residues: 39.8157 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 : 0.303 ------------------------------------------------------------------------------- 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... 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 = 0.196076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170894 restraints weight = 30828.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175592 restraints weight = 13486.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.178633 restraints weight = 7700.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180453 restraints weight = 5179.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181708 restraints weight = 3979.760| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 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 = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2237 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= 0.145 Angle : 0.569 4.799 9448 Z= 0.303 Chirality : 0.040 0.158 1015 Planarity : 0.005 0.040 1173 Dihedral : 12.300 172.315 1044 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.14 % Favored : 92.23 % Rotamer: Outliers : 1.58 % Allowed : 8.78 % 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 0.011 0.001 TYR C 178 PHE 0.014 0.001 PHE B 198 TRP 0.004 0.001 TRP B 91 HIS 0.003 0.001 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6946) covalent geometry : angle 0.56883 / 0.30 ( 9448) hydrogen bonds : bond 0.04662 / 2.85 ( 247) hydrogen bonds : angle 5.36281 / 3.79 ( 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 156 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.282 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: 0.6623 (p0) cc_final: 0.6136 (p0) REVERT: B 92 ASP cc_start: 0.8044 (p0) cc_final: 0.7768 (p0) REVERT: C 175 MET cc_start: 0.4116 (mtt) cc_final: 0.3865 (mtt) REVERT: C 188 MET cc_start: 0.6949 (mmp) cc_final: 0.6527 (mmt) REVERT: D 4 THR cc_start: 0.8364 (p) cc_final: 0.8118 (t) outliers start: 11 outliers final: 10 residues processed: 149 average time/residue: 0.1488 time to fit residues: 29.6582 Evaluate side-chains 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164000 restraints weight = 31226.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168591 restraints weight = 14176.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171384 restraints weight = 8423.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173453 restraints weight = 5904.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174529 restraints weight = 4613.267| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 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 = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6946 Z= 0.201 Angle : 0.604 4.843 9448 Z= 0.326 Chirality : 0.041 0.179 1015 Planarity : 0.005 0.039 1173 Dihedral : 12.334 172.542 1044 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.90 % Favored : 90.73 % Rotamer: Outliers : 2.88 % Allowed : 11.51 % Favored : 85.61 % 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: -2.21 (0.28), residues: 798 helix: -0.13 (0.31), residues: 281 sheet: -0.76 (0.45), residues: 119 loop : -2.79 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.013 0.002 TYR B 140 PHE 0.014 0.002 PHE A 205 TRP 0.007 0.001 TRP A 248 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 6946) covalent geometry : angle 0.60412 / 0.33 ( 9448) hydrogen bonds : bond 0.04871 / 3.00 ( 247) hydrogen bonds : angle 5.39829 / 3.84 ( 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 151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.246 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 272 ASP cc_start: 0.6784 (p0) cc_final: 0.6289 (p0) REVERT: B 92 ASP cc_start: 0.8133 (p0) cc_final: 0.7823 (p0) REVERT: C 188 MET cc_start: 0.6988 (mmp) cc_final: 0.6493 (mmt) REVERT: D 4 THR cc_start: 0.8349 (p) cc_final: 0.8089 (t) outliers start: 20 outliers final: 17 residues processed: 139 average time/residue: 0.1661 time to fit residues: 30.8035 Evaluate side-chains 144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.194026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168031 restraints weight = 31448.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172532 restraints weight = 14601.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.175480 restraints weight = 8769.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177080 restraints weight = 6125.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.178450 restraints weight = 4883.121| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3050 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= 0.123 Angle : 0.540 4.660 9448 Z= 0.286 Chirality : 0.039 0.187 1015 Planarity : 0.004 0.035 1173 Dihedral : 12.208 175.013 1044 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.15 % Favored : 91.35 % Rotamer: Outliers : 2.30 % Allowed : 14.10 % Favored : 83.60 % 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: -1.97 (0.29), residues: 798 helix: 0.14 (0.32), residues: 281 sheet: -0.72 (0.46), residues: 119 loop : -2.67 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR B 140 PHE 0.012 0.001 PHE B 110 TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6946) covalent geometry : angle 0.53970 / 0.29 ( 9448) hydrogen bonds : bond 0.03826 / 2.39 ( 247) hydrogen bonds : angle 4.98051 / 3.55 ( 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 147 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.273 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: 0.8005 (p0) cc_final: 0.7710 (p0) REVERT: C 188 MET cc_start: 0.6989 (mmp) cc_final: 0.6465 (mmt) REVERT: D 4 THR cc_start: 0.8350 (p) cc_final: 0.8119 (t) outliers start: 16 outliers final: 13 residues processed: 139 average time/residue: 0.1515 time to fit residues: 28.8634 Evaluate side-chains 140 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.191323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164820 restraints weight = 31481.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169458 restraints weight = 14224.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172418 restraints weight = 8393.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.174333 restraints weight = 5847.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.175053 restraints weight = 4575.976| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6946 Z= 0.165 Angle : 0.566 4.507 9448 Z= 0.300 Chirality : 0.040 0.182 1015 Planarity : 0.005 0.037 1173 Dihedral : 12.216 172.670 1044 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.65 % Favored : 89.85 % Rotamer: Outliers : 3.02 % Allowed : 15.40 % Favored : 81.58 % 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: -2.00 (0.29), residues: 798 helix: 0.04 (0.32), residues: 287 sheet: -0.78 (0.47), residues: 119 loop : -2.65 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.013 0.001 TYR B 140 PHE 0.011 0.001 PHE B 110 TRP 0.006 0.001 TRP A 248 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6946) covalent geometry : angle 0.56577 / 0.30 ( 9448) hydrogen bonds : bond 0.04122 / 2.57 ( 247) hydrogen bonds : angle 5.04963 / 3.60 ( 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 151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.318 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: A 275 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6506 (tmm) REVERT: B 92 ASP cc_start: 0.8047 (p0) cc_final: 0.7710 (p0) REVERT: C 188 MET cc_start: 0.6961 (mmp) cc_final: 0.6337 (mmt) REVERT: D 4 THR cc_start: 0.8310 (p) cc_final: 0.8062 (t) outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 0.1506 time to fit residues: 28.2385 Evaluate side-chains 146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.192586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166565 restraints weight = 31201.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171011 restraints weight = 14539.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173952 restraints weight = 8776.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175737 restraints weight = 6144.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176975 restraints weight = 4854.679| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6946 Z= 0.116 Angle : 0.531 4.408 9448 Z= 0.280 Chirality : 0.039 0.184 1015 Planarity : 0.004 0.037 1173 Dihedral : 12.131 174.564 1044 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.40 % Favored : 90.98 % Rotamer: Outliers : 2.30 % Allowed : 16.12 % Favored : 81.58 % 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: 0.25 (0.32), residues: 288 sheet: -0.66 (0.48), residues: 119 loop : -2.53 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.013 0.001 TYR C 167 PHE 0.014 0.001 PHE B 110 TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6946) covalent geometry : angle 0.53138 / 0.28 ( 9448) hydrogen bonds : bond 0.03574 / 2.24 ( 247) hydrogen bonds : angle 4.78315 / 3.41 ( 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 148 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.235 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: 0.7094 (OUTLIER) cc_final: 0.6452 (tmm) REVERT: B 92 ASP cc_start: 0.8042 (p0) cc_final: 0.7741 (p0) REVERT: C 188 MET cc_start: 0.6928 (mmp) cc_final: 0.6307 (mmt) REVERT: D 4 THR cc_start: 0.8324 (p) cc_final: 0.8096 (t) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.1308 time to fit residues: 24.8534 Evaluate side-chains 141 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 114 SER Chi-restraints excluded: chain B residue 163 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: 6.9990 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: 2.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.190146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163604 restraints weight = 31499.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168198 restraints weight = 14431.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171109 restraints weight = 8596.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173123 restraints weight = 6038.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174250 restraints weight = 4679.191| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6946 Z= 0.159 Angle : 0.562 4.496 9448 Z= 0.297 Chirality : 0.040 0.176 1015 Planarity : 0.005 0.037 1173 Dihedral : 12.167 172.043 1044 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.03 % Favored : 89.35 % Rotamer: Outliers : 2.88 % Allowed : 15.68 % Favored : 81.44 % 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: -1.78 (0.29), residues: 798 helix: 0.33 (0.32), residues: 282 sheet: -0.81 (0.47), residues: 121 loop : -2.53 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.013 0.001 TYR B 140 PHE 0.017 0.001 PHE B 110 TRP 0.006 0.001 TRP A 248 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6946) covalent geometry : angle 0.56173 / 0.30 ( 9448) hydrogen bonds : bond 0.04005 / 2.50 ( 247) hydrogen bonds : angle 4.91500 / 3.50 ( 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 149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.210 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: 0.8069 (p0) cc_final: 0.7706 (p0) REVERT: C 188 MET cc_start: 0.6960 (mmp) cc_final: 0.6496 (mmt) REVERT: D 4 THR cc_start: 0.8330 (p) cc_final: 0.8085 (t) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.1512 time to fit residues: 28.6170 Evaluate side-chains 145 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.191781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165480 restraints weight = 31321.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170010 restraints weight = 14775.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172953 restraints weight = 8808.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174643 restraints weight = 6212.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175708 restraints weight = 4965.780| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 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 = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3704 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= 0.121 Angle : 0.535 4.609 9448 Z= 0.281 Chirality : 0.039 0.180 1015 Planarity : 0.004 0.037 1173 Dihedral : 12.099 173.604 1044 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.90 % Favored : 90.48 % Rotamer: Outliers : 2.30 % Allowed : 16.69 % Favored : 81.01 % 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: -1.65 (0.29), residues: 798 helix: 0.36 (0.32), residues: 291 sheet: -0.60 (0.49), residues: 109 loop : -2.45 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.012 0.001 TYR A 277 PHE 0.014 0.001 PHE B 110 TRP 0.005 0.001 TRP C 190 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6946) covalent geometry : angle 0.53513 / 0.28 ( 9448) hydrogen bonds : bond 0.03581 / 2.25 ( 247) hydrogen bonds : angle 4.73372 / 3.36 ( 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 146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.326 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: 0.8060 (p0) cc_final: 0.7698 (p0) REVERT: C 188 MET cc_start: 0.6927 (mmp) cc_final: 0.6425 (mmt) REVERT: D 4 THR cc_start: 0.8336 (p) cc_final: 0.8101 (t) outliers start: 16 outliers final: 15 residues processed: 140 average time/residue: 0.1404 time to fit residues: 26.8637 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 : 0.387 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.191449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165122 restraints weight = 31570.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169809 restraints weight = 14368.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172743 restraints weight = 8455.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.174726 restraints weight = 5882.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175675 restraints weight = 4574.277| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 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 = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.003 0.033 6946 Z= 0.121 Angle : 0.534 4.721 9448 Z= 0.280 Chirality : 0.039 0.174 1015 Planarity : 0.004 0.038 1173 Dihedral : 12.060 172.316 1044 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.15 % Favored : 89.22 % Rotamer: Outliers : 2.30 % Allowed : 17.55 % Favored : 80.14 % 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: -1.53 (0.30), residues: 798 helix: 0.45 (0.32), residues: 291 sheet: -0.57 (0.49), residues: 109 loop : -2.37 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.012 0.001 TYR A 277 PHE 0.013 0.001 PHE B 110 TRP 0.007 0.001 TRP C 190 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6946) covalent geometry : angle 0.53449 / 0.28 ( 9448) hydrogen bonds : bond 0.03498 / 2.19 ( 247) hydrogen bonds : angle 4.64309 / 3.30 ( 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 146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.340 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: 0.7333 (tmm) cc_final: 0.6633 (tmm) REVERT: B 92 ASP cc_start: 0.8049 (p0) cc_final: 0.7713 (p0) REVERT: C 188 MET cc_start: 0.6881 (mmp) cc_final: 0.6377 (mmt) REVERT: D 4 THR cc_start: 0.8356 (p) cc_final: 0.8146 (t) outliers start: 16 outliers final: 14 residues processed: 140 average time/residue: 0.1336 time to fit residues: 25.8243 Evaluate side-chains 144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.191835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165586 restraints weight = 31549.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170305 restraints weight = 14286.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173300 restraints weight = 8334.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174761 restraints weight = 5743.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176299 restraints weight = 4643.310| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3864 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= 0.115 Angle : 0.530 4.800 9448 Z= 0.276 Chirality : 0.039 0.169 1015 Planarity : 0.005 0.088 1173 Dihedral : 12.027 172.206 1044 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.77 % Favored : 90.73 % Rotamer: Outliers : 2.16 % Allowed : 17.55 % Favored : 80.29 % 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: -1.38 (0.30), residues: 798 helix: 0.66 (0.32), residues: 286 sheet: -0.71 (0.48), residues: 119 loop : -2.27 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.012 0.001 TYR A 277 PHE 0.012 0.001 PHE B 110 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6946) covalent geometry : angle 0.52956 / 0.28 ( 9448) hydrogen bonds : bond 0.03370 / 2.11 ( 247) hydrogen bonds : angle 4.56581 / 3.24 ( 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 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.311 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: 0.7381 (tmm) cc_final: 0.6620 (tmm) REVERT: B 92 ASP cc_start: 0.8003 (p0) cc_final: 0.7650 (p0) REVERT: C 188 MET cc_start: 0.6863 (mmp) cc_final: 0.6367 (mmt) outliers start: 15 outliers final: 15 residues processed: 138 average time/residue: 0.1375 time to fit residues: 26.1730 Evaluate side-chains 140 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 78 PHE 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: 0.9980 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.192087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166034 restraints weight = 31181.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170524 restraints weight = 14526.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173399 restraints weight = 8692.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175064 restraints weight = 6114.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176370 restraints weight = 4852.634| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3946 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= 0.111 Angle : 0.531 4.651 9448 Z= 0.275 Chirality : 0.039 0.167 1015 Planarity : 0.005 0.093 1173 Dihedral : 12.008 171.882 1044 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.52 % Favored : 89.97 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % 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: -1.27 (0.30), residues: 798 helix: 0.72 (0.32), residues: 286 sheet: -0.32 (0.50), residues: 109 loop : -2.26 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.012 0.001 TYR A 277 PHE 0.012 0.001 PHE B 110 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6946) covalent geometry : angle 0.53068 / 0.28 ( 9448) hydrogen bonds : bond 0.03302 / 2.07 ( 247) hydrogen bonds : angle 4.51133 / 3.20 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.66 seconds wall clock time: 40 minutes 34.23 seconds (2434.23 seconds total)