Starting phenix.real_space_refine on Mon Jan 13 14:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymk_39396/01_2025/8ymk_39396.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.007 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 1752 2.51 5 N 487 2.21 5 O 481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2744 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1355 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 22, 'TRANS': 203} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1389 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 22, 'TRANS': 203} Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 182 Time building chain proxies: 2.77, per 1000 atoms: 1.01 Number of scatterers: 2744 At special positions: 0 Unit cell: (104.94, 76.32, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 481 8.00 N 487 7.00 C 1752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS B 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 147 " distance=2.34 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: 0.74 Conformation dependent library (CDL) restraints added in 399.3 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 844 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 60.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.765A pdb=" N ASP A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 101 removed outlier: 3.772A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 4.196A pdb=" N GLU A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.687A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 4.107A pdb=" N SER A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.102A pdb=" N ILE A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 44 removed outlier: 3.562A pdb=" N SER B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Proline residue: B 11 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.579A pdb=" N THR B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU B 39 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 102 removed outlier: 4.444A pdb=" N LEU B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 171 through 185 removed outlier: 3.911A pdb=" N LEU B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.154A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 195 " --> pdb=" O TRP B 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 4.065A pdb=" N LEU B 205 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 215 through 226 removed outlier: 3.880A pdb=" N PHE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 840 1.34 - 1.46: 522 1.46 - 1.58: 1421 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 2807 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.533 1.462 0.071 1.58e-02 4.01e+03 2.02e+01 bond pdb=" C SER A 31 " pdb=" O SER A 31 " ideal model delta sigma weight residual 1.234 1.291 -0.057 1.35e-02 5.49e+03 1.76e+01 bond pdb=" CA CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sigma weight residual 1.522 1.543 -0.020 7.00e-03 2.04e+04 8.57e+00 bond pdb=" N ILE A 28 " pdb=" CA ILE A 28 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 8.12e+00 bond pdb=" N GLN B 129 " pdb=" CA GLN B 129 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.33e-02 5.65e+03 6.75e+00 ... (remaining 2802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 3702 2.53 - 5.06: 146 5.06 - 7.58: 28 7.58 - 10.11: 9 10.11 - 12.64: 4 Bond angle restraints: 3889 Sorted by residual: angle pdb=" C ILE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta sigma weight residual 119.85 131.60 -11.75 1.01e+00 9.80e-01 1.35e+02 angle pdb=" C ILE B 150 " pdb=" N PRO B 151 " pdb=" CA PRO B 151 " ideal model delta sigma weight residual 119.85 131.02 -11.17 1.01e+00 9.80e-01 1.22e+02 angle pdb=" N CYS B 138 " pdb=" CA CYS B 138 " pdb=" C CYS B 138 " ideal model delta sigma weight residual 111.14 100.67 10.47 1.08e+00 8.57e-01 9.40e+01 angle pdb=" N TRP A 156 " pdb=" CA TRP A 156 " pdb=" C TRP A 156 " ideal model delta sigma weight residual 110.30 97.66 12.64 1.50e+00 4.44e-01 7.10e+01 angle pdb=" C ILE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.85 126.95 -7.10 1.01e+00 9.80e-01 4.94e+01 ... (remaining 3884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 1477 17.32 - 34.64: 67 34.64 - 51.96: 24 51.96 - 69.28: 2 69.28 - 86.60: 2 Dihedral angle restraints: 1572 sinusoidal: 273 harmonic: 1299 Sorted by residual: dihedral pdb=" CB CYS B 48 " pdb=" SG CYS B 48 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual 93.00 179.60 -86.60 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual -86.00 -133.03 47.03 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS B 139 " pdb=" SG CYS B 139 " pdb=" SG CYS B 147 " pdb=" CB CYS B 147 " ideal model delta sinusoidal sigma weight residual -86.00 -130.16 44.16 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 1569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 381 0.072 - 0.143: 70 0.143 - 0.215: 9 0.215 - 0.286: 6 0.286 - 0.358: 1 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA CYS B 137 " pdb=" N CYS B 137 " pdb=" C CYS B 137 " pdb=" CB CYS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA CYS B 138 " pdb=" N CYS B 138 " pdb=" C CYS B 138 " pdb=" CB CYS B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO B 135 " pdb=" N PRO B 135 " pdb=" C PRO B 135 " pdb=" CB PRO B 135 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 464 not shown) Planarity restraints: 503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 33 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASP A 33 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP A 33 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 34 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 83 " -0.022 2.00e-02 2.50e+03 2.37e-02 9.87e+00 pdb=" CG PHE B 83 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 83 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 83 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 83 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 177 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 178 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " 0.025 5.00e-02 4.00e+02 ... (remaining 500 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 886 2.82 - 3.34: 2859 3.34 - 3.86: 4083 3.86 - 4.38: 4076 4.38 - 4.90: 6427 Nonbonded interactions: 18331 Sorted by model distance: nonbonded pdb=" O SER A 34 " pdb=" N THR A 37 " model vdw 2.296 3.120 nonbonded pdb=" O ALA A 166 " pdb=" CB PHE A 170 " model vdw 2.348 3.440 nonbonded pdb=" O LEU B 209 " pdb=" N LEU B 213 " model vdw 2.357 3.120 nonbonded pdb=" O GLY A 43 " pdb=" N LEU B 49 " model vdw 2.366 3.120 nonbonded pdb=" O SER A 34 " pdb=" C TRP A 35 " model vdw 2.378 3.270 ... (remaining 18326 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 'A' and (resid 1 through 40 or (resid 41 through 42 and (name N or name C \ A or name C or name O or name CB )) or resid 43 through 79 or (resid 80 and (nam \ e N or name CA or name C or name O or name CB )) or resid 81 through 205 or (res \ id 206 through 220 and (name N or name CA or name C or name O or name CB )) or r \ esid 221 through 226)) selection = (chain 'B' and ((resid 1 through 27 and (name N or name CA or name C or name O o \ r name CB )) or resid 28 through 76 or (resid 77 and (name N or name CA or name \ C or name O or name CB )) or resid 78 through 92 or (resid 93 and (name N or nam \ e CA or name C or name O or name CB )) or resid 94 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 173 or (resid 174 through 181 and (name N or name CA or name C or nam \ e O or name CB )) or resid 182 through 214 or (resid 215 through 220 and (name N \ or name CA or name C or name O or name CB )) or resid 221 through 226)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 2807 Z= 0.324 Angle : 1.217 12.638 3889 Z= 0.844 Chirality : 0.061 0.358 467 Planarity : 0.005 0.055 503 Dihedral : 11.932 72.533 701 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 1.56 % Allowed : 14.06 % Favored : 84.38 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.43), residues: 448 helix: 0.90 (0.35), residues: 243 sheet: None (None), residues: 0 loop : -3.98 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 36 PHE 0.055 0.002 PHE B 83 TYR 0.004 0.001 TYR B 100 ARG 0.019 0.004 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 CYS cc_start: 0.9015 (t) cc_final: 0.8644 (m) REVERT: B 33 ASP cc_start: 0.8820 (m-30) cc_final: 0.8605 (m-30) REVERT: B 36 TRP cc_start: 0.9553 (m100) cc_final: 0.8961 (t-100) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1442 time to fit residues: 14.6483 Evaluate side-chains 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.3350 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.123145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.109554 restraints weight = 23058.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.109094 restraints weight = 23454.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.109962 restraints weight = 23352.404| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2807 Z= 0.247 Angle : 0.848 9.479 3889 Z= 0.425 Chirality : 0.053 0.414 467 Planarity : 0.006 0.066 503 Dihedral : 5.906 29.907 458 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 1.56 % Allowed : 10.49 % Favored : 87.95 % Rotamer: Outliers : 6.02 % Allowed : 24.81 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.41), residues: 448 helix: 0.96 (0.33), residues: 247 sheet: None (None), residues: 0 loop : -4.32 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 36 PHE 0.052 0.003 PHE B 83 TYR 0.010 0.002 TYR A 206 ARG 0.008 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.311 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 0.0805 time to fit residues: 6.5297 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 0.0070 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.121395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.107953 restraints weight = 23041.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.107676 restraints weight = 23107.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.107919 restraints weight = 23471.222| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2807 Z= 0.201 Angle : 0.807 11.732 3889 Z= 0.395 Chirality : 0.049 0.235 467 Planarity : 0.006 0.088 503 Dihedral : 5.600 26.872 458 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 1.56 % Allowed : 10.94 % Favored : 87.50 % Rotamer: Outliers : 3.76 % Allowed : 27.07 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.42), residues: 448 helix: 1.15 (0.34), residues: 247 sheet: None (None), residues: 0 loop : -4.33 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 36 PHE 0.039 0.003 PHE B 83 TYR 0.003 0.001 TYR A 206 ARG 0.009 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.317 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.0978 time to fit residues: 7.2476 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.119728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.106717 restraints weight = 23240.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.107007 restraints weight = 22654.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.107203 restraints weight = 22981.313| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2807 Z= 0.205 Angle : 0.851 13.459 3889 Z= 0.401 Chirality : 0.049 0.286 467 Planarity : 0.005 0.063 503 Dihedral : 5.472 26.036 458 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 1.56 % Allowed : 11.38 % Favored : 87.05 % Rotamer: Outliers : 6.02 % Allowed : 27.07 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.42), residues: 448 helix: 1.27 (0.34), residues: 247 sheet: None (None), residues: 0 loop : -4.24 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 PHE 0.039 0.003 PHE A 85 TYR 0.006 0.001 TYR A 206 ARG 0.009 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 37 THR cc_start: 0.8917 (m) cc_final: 0.8700 (p) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0815 time to fit residues: 6.6218 Evaluate side-chains 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 0.0050 chunk 2 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.107298 restraints weight = 23462.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.107312 restraints weight = 23322.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.107435 restraints weight = 23709.262| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2807 Z= 0.203 Angle : 0.869 11.645 3889 Z= 0.410 Chirality : 0.054 0.364 467 Planarity : 0.005 0.050 503 Dihedral : 5.288 25.134 458 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 1.56 % Allowed : 10.94 % Favored : 87.50 % Rotamer: Outliers : 5.26 % Allowed : 30.83 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.42), residues: 448 helix: 1.33 (0.34), residues: 248 sheet: None (None), residues: 0 loop : -4.19 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 PHE 0.058 0.004 PHE A 85 TYR 0.019 0.001 TYR A 206 ARG 0.007 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 37 THR cc_start: 0.8964 (m) cc_final: 0.8732 (p) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.0922 time to fit residues: 7.2397 Evaluate side-chains 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.0020 overall best weight: 0.3202 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.121331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.108090 restraints weight = 23433.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.107918 restraints weight = 22925.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.108248 restraints weight = 23689.866| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2807 Z= 0.196 Angle : 0.864 14.224 3889 Z= 0.406 Chirality : 0.051 0.323 467 Planarity : 0.004 0.046 503 Dihedral : 5.114 24.942 458 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 1.56 % Allowed : 10.49 % Favored : 87.95 % Rotamer: Outliers : 2.26 % Allowed : 36.84 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.42), residues: 448 helix: 1.39 (0.34), residues: 246 sheet: None (None), residues: 0 loop : -4.02 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 PHE 0.059 0.004 PHE B 83 TYR 0.010 0.001 TYR A 206 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 37 THR cc_start: 0.9055 (m) cc_final: 0.8836 (p) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.0816 time to fit residues: 6.3393 Evaluate side-chains 54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 139 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.102000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.083757 restraints weight = 16334.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.083174 restraints weight = 17878.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.082839 restraints weight = 20758.833| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2807 Z= 0.194 Angle : 0.905 17.448 3889 Z= 0.419 Chirality : 0.054 0.309 467 Planarity : 0.004 0.046 503 Dihedral : 4.994 24.535 458 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.56 % Allowed : 11.38 % Favored : 87.05 % Rotamer: Outliers : 3.76 % Allowed : 39.10 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.43), residues: 448 helix: 1.57 (0.35), residues: 241 sheet: None (None), residues: 0 loop : -3.88 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 PHE 0.055 0.003 PHE A 85 TYR 0.024 0.001 TYR A 206 ARG 0.006 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.294 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.0810 time to fit residues: 6.1290 Evaluate side-chains 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 139 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.110516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.098459 restraints weight = 23869.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.098089 restraints weight = 21681.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.098332 restraints weight = 23679.593| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 2807 Z= 0.343 Angle : 1.007 12.797 3889 Z= 0.516 Chirality : 0.062 0.331 467 Planarity : 0.006 0.059 503 Dihedral : 6.264 25.623 458 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 1.56 % Allowed : 15.85 % Favored : 82.59 % Rotamer: Outliers : 7.52 % Allowed : 36.84 % Favored : 55.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.41), residues: 448 helix: 0.73 (0.33), residues: 255 sheet: None (None), residues: 0 loop : -4.13 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 35 PHE 0.042 0.004 PHE A 85 TYR 0.011 0.002 TYR A 206 ARG 0.010 0.002 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0832 time to fit residues: 6.0632 Evaluate side-chains 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 163 TRP Chi-restraints excluded: chain B residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.0020 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 1.5406 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.113084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.101015 restraints weight = 23624.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.100793 restraints weight = 22050.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.101203 restraints weight = 21863.979| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2807 Z= 0.224 Angle : 1.020 16.059 3889 Z= 0.478 Chirality : 0.058 0.343 467 Planarity : 0.004 0.046 503 Dihedral : 5.947 26.536 458 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 1.56 % Allowed : 13.39 % Favored : 85.04 % Rotamer: Outliers : 5.26 % Allowed : 39.85 % Favored : 54.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.42), residues: 448 helix: 1.29 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -4.10 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 223 PHE 0.058 0.003 PHE A 85 TYR 0.006 0.001 TYR A 206 ARG 0.007 0.002 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.373 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0878 time to fit residues: 6.4489 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 163 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 30.0000 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.112715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.100911 restraints weight = 23466.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.100548 restraints weight = 22932.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.100832 restraints weight = 22788.650| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 2807 Z= 0.230 Angle : 1.048 17.082 3889 Z= 0.484 Chirality : 0.058 0.347 467 Planarity : 0.004 0.046 503 Dihedral : 5.669 25.904 458 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 1.34 % Allowed : 14.29 % Favored : 84.38 % Rotamer: Outliers : 5.26 % Allowed : 42.11 % Favored : 52.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.43), residues: 448 helix: 1.32 (0.35), residues: 254 sheet: None (None), residues: 0 loop : -3.93 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 PHE 0.055 0.003 PHE A 85 TYR 0.004 0.001 TYR A 225 ARG 0.006 0.001 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 56 average time/residue: 0.0826 time to fit residues: 6.2757 Evaluate side-chains 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 163 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 43 optimal weight: 0.0040 chunk 32 optimal weight: 6.9990 overall best weight: 0.2646 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.115147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.102951 restraints weight = 23056.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.102542 restraints weight = 25076.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104248 restraints weight = 18892.442| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 2807 Z= 0.210 Angle : 1.075 17.104 3889 Z= 0.482 Chirality : 0.058 0.362 467 Planarity : 0.004 0.045 503 Dihedral : 5.282 25.693 458 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.94 % Favored : 87.72 % Rotamer: Outliers : 4.51 % Allowed : 42.86 % Favored : 52.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.43), residues: 448 helix: 1.57 (0.35), residues: 243 sheet: None (None), residues: 0 loop : -3.79 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 PHE 0.062 0.003 PHE A 85 TYR 0.003 0.001 TYR A 206 ARG 0.003 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.20 seconds wall clock time: 25 minutes 27.66 seconds (1527.66 seconds total)