Starting phenix.real_space_refine on Wed Oct 9 13:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_39396.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_39396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_39396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_39396.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymk_39396/10_2024/8ymk_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-5477/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: 2.79, per 1000 atoms: 1.02 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: 0.90 Conformation dependent library (CDL) restraints added in 453.4 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: 0.22 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: 0.61 Time building geometry restraints manager: 0.88 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.333 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: 0.1158 time to fit residues: 11.4248 Evaluate side-chains 55 residues out of total 412 non-(ALA, GLY, PRO) need fitting. 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 0.0868 time to fit residues: 6.9670 Evaluate side-chains 56 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 22 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2807 Z= 0.268 Angle : 0.817 11.341 3889 Z= 0.422 Chirality : 0.050 0.198 467 Planarity : 0.006 0.096 503 Dihedral : 6.005 27.416 458 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 1.56 % Allowed : 14.29 % Favored : 84.15 % Rotamer: Outliers : 5.26 % Allowed : 25.56 % 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: -1.93 (0.41), residues: 448 helix: 0.91 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -4.32 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 36 PHE 0.038 0.004 PHE B 83 TYR 0.009 0.001 TYR A 206 ARG 0.007 0.002 ARG A 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 fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.0811 time to fit residues: 6.1610 Evaluate side-chains 58 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE 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 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2807 Z= 0.270 Angle : 0.837 10.504 3889 Z= 0.420 Chirality : 0.051 0.259 467 Planarity : 0.005 0.079 503 Dihedral : 6.005 27.295 458 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 1.56 % Allowed : 14.06 % Favored : 84.38 % Rotamer: Outliers : 7.52 % Allowed : 26.32 % Favored : 66.17 % 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: -1.78 (0.41), residues: 448 helix: 1.04 (0.34), residues: 245 sheet: None (None), residues: 0 loop : -4.31 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 35 PHE 0.030 0.003 PHE B 83 TYR 0.016 0.002 TYR A 206 ARG 0.013 0.004 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 62 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1022 time to fit residues: 7.7242 Evaluate side-chains 57 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE 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 95 LEU Chi-restraints excluded: chain B residue 139 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.0010 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 50.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2807 Z= 0.199 Angle : 0.869 13.612 3889 Z= 0.414 Chirality : 0.054 0.353 467 Planarity : 0.005 0.056 503 Dihedral : 5.823 25.862 458 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 1.56 % Allowed : 12.72 % Favored : 85.71 % Rotamer: Outliers : 6.77 % Allowed : 33.08 % Favored : 60.15 % 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: -1.46 (0.42), residues: 448 helix: 1.36 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -4.21 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 PHE 0.060 0.003 PHE A 85 TYR 0.012 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 62 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.325 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.0948 time to fit residues: 7.3396 Evaluate side-chains 59 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 163 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.0070 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2807 Z= 0.203 Angle : 0.908 15.993 3889 Z= 0.421 Chirality : 0.053 0.368 467 Planarity : 0.004 0.047 503 Dihedral : 5.450 25.836 458 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 1.56 % Allowed : 12.05 % Favored : 86.38 % Rotamer: Outliers : 3.76 % Allowed : 35.34 % 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: -1.35 (0.42), residues: 448 helix: 1.37 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -4.04 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 PHE 0.062 0.003 PHE B 83 TYR 0.016 0.001 TYR A 206 ARG 0.006 0.002 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 62 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.306 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.0857 time to fit residues: 7.0464 Evaluate side-chains 56 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 0.0270 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2807 Z= 0.290 Angle : 0.908 12.841 3889 Z= 0.459 Chirality : 0.054 0.272 467 Planarity : 0.005 0.060 503 Dihedral : 6.038 25.435 458 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 1.56 % Allowed : 14.51 % Favored : 83.93 % Rotamer: Outliers : 7.52 % Allowed : 36.09 % Favored : 56.39 % 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: -1.60 (0.42), residues: 448 helix: 1.01 (0.34), residues: 253 sheet: None (None), residues: 0 loop : -4.17 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 PHE 0.031 0.003 PHE B 83 TYR 0.010 0.001 TYR A 206 ARG 0.007 0.002 ARG A 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 61 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.341 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1001 time to fit residues: 7.4366 Evaluate side-chains 57 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 163 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2807 Z= 0.250 Angle : 0.943 15.237 3889 Z= 0.457 Chirality : 0.053 0.313 467 Planarity : 0.004 0.046 503 Dihedral : 6.023 27.755 458 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % Rotamer: Outliers : 6.02 % Allowed : 39.10 % 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: -1.49 (0.42), residues: 448 helix: 1.09 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -4.13 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 PHE 0.018 0.002 PHE B 83 TYR 0.013 0.001 TYR A 206 ARG 0.007 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 59 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.0992 time to fit residues: 7.3569 Evaluate side-chains 58 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 90 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 3 optimal weight: 0.0170 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 2807 Z= 0.235 Angle : 0.960 15.936 3889 Z= 0.456 Chirality : 0.055 0.312 467 Planarity : 0.004 0.045 503 Dihedral : 5.761 26.064 458 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 1.34 % Allowed : 13.84 % Favored : 84.82 % 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: -1.38 (0.42), residues: 448 helix: 1.17 (0.34), residues: 253 sheet: None (None), residues: 0 loop : -4.06 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 PHE 0.027 0.002 PHE B 83 TYR 0.012 0.001 TYR A 206 ARG 0.006 0.001 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 59 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.0984 time to fit residues: 7.4746 Evaluate side-chains 59 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 26 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 2807 Z= 0.212 Angle : 0.998 17.196 3889 Z= 0.460 Chirality : 0.056 0.358 467 Planarity : 0.004 0.045 503 Dihedral : 5.445 26.892 458 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.71 % Favored : 87.95 % 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: -1.24 (0.42), residues: 448 helix: 1.26 (0.34), residues: 249 sheet: None (None), residues: 0 loop : -3.85 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 PHE 0.024 0.002 PHE B 83 TYR 0.015 0.001 TYR A 206 ARG 0.003 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 fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.0852 time to fit residues: 6.3287 Evaluate side-chains 59 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE 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 4 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 17 optimal weight: 0.2980 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.112312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.100705 restraints weight = 24216.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.100455 restraints weight = 25250.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.100778 restraints weight = 23505.705| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.6888 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= 0.209 Angle : 0.974 17.479 3889 Z= 0.450 Chirality : 0.055 0.338 467 Planarity : 0.004 0.045 503 Dihedral : 5.217 25.398 458 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.34 % Allowed : 12.28 % Favored : 86.38 % Rotamer: Outliers : 5.26 % Allowed : 41.35 % Favored : 53.38 % 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: -1.08 (0.43), residues: 448 helix: 1.39 (0.35), residues: 249 sheet: None (None), residues: 0 loop : -3.76 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 PHE 0.025 0.002 PHE B 83 TYR 0.005 0.001 TYR A 206 ARG 0.004 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1016.52 seconds wall clock time: 20 minutes 28.18 seconds (1228.18 seconds total)