Starting phenix.real_space_refine on Thu Nov 14 20:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/11_2024/8iu0_35713.cif" } resolution = 2.66 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= 0.004 sd= 0.125 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 60 5.16 5 C 4863 2.51 5 N 954 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 35 " occ=0.50 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 35 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 35 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 5.22, per 1000 atoms: 0.74 Number of scatterers: 7062 At special positions: 0 Unit cell: (77.19, 77.19, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 9 15.00 O 1176 8.00 N 954 7.00 C 4863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 426 hydrogen bonds defined for protein. 1281 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: 1.97 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1226 1.33 - 1.46: 2621 1.46 - 1.59: 3260 1.59 - 1.72: 15 1.72 - 1.85: 81 Bond restraints: 7203 Sorted by residual: bond pdb=" C7 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC A 311 " pdb=" C4 PSC A 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC B 311 " pdb=" C4 PSC B 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC C 311 " pdb=" C4 PSC C 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 1.530 1.320 0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 9164 3.02 - 6.03: 409 6.03 - 9.05: 18 9.05 - 12.07: 21 12.07 - 15.08: 18 Bond angle restraints: 9630 Sorted by residual: angle pdb=" C10 PSC B 310 " pdb=" C9 PSC B 310 " pdb=" C8 PSC B 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC A 310 " pdb=" C9 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC C 310 " pdb=" C9 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 127.68 112.61 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC B 310 " pdb=" C11 PSC B 310 " pdb=" C12 PSC B 310 " ideal model delta sigma weight residual 111.07 126.14 -15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC A 310 " pdb=" C11 PSC A 310 " pdb=" C12 PSC A 310 " ideal model delta sigma weight residual 111.07 126.12 -15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 9625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3708 23.98 - 47.95: 324 47.95 - 71.93: 108 71.93 - 95.90: 0 95.90 - 119.88: 3 Dihedral angle restraints: 4143 sinusoidal: 1890 harmonic: 2253 Sorted by residual: dihedral pdb=" C03 PSC C 302 " pdb=" O11 PSC C 302 " pdb=" P PSC C 302 " pdb=" O12 PSC C 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.58 119.88 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC A 302 " pdb=" O11 PSC A 302 " pdb=" P PSC A 302 " pdb=" O12 PSC A 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.59 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC B 302 " pdb=" O11 PSC B 302 " pdb=" P PSC B 302 " pdb=" O12 PSC B 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.60 119.86 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 457 0.051 - 0.102: 326 0.102 - 0.153: 113 0.153 - 0.204: 31 0.204 - 0.255: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 147 " pdb=" N PRO C 147 " pdb=" C PRO C 147 " pdb=" CB PRO C 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 933 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C11 PSC B 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC B 312 " -0.100 2.00e-02 2.50e+03 pdb=" C9 PSC B 312 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC A 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC A 312 " -0.099 2.00e-02 2.50e+03 pdb=" C9 PSC A 312 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 312 " 0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC C 312 " -0.102 2.00e-02 2.50e+03 pdb=" C8 PSC C 312 " 0.099 2.00e-02 2.50e+03 pdb=" C9 PSC C 312 " -0.307 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1588 2.79 - 3.32: 6677 3.32 - 3.84: 12411 3.84 - 4.37: 15914 4.37 - 4.90: 25235 Nonbonded interactions: 61825 Sorted by model distance: nonbonded pdb=" OH TYR A 103 " pdb=" O HOH A 401 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 103 " pdb=" O HOH C 401 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 103 " pdb=" O HOH B 401 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 309 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG A 171 " pdb=" O13 PSC A 309 " model vdw 2.306 3.120 ... (remaining 61820 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 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'B' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'C' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.590 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:15.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.014 0.211 7203 Z= 0.870 Angle : 1.596 15.084 9630 Z= 0.937 Chirality : 0.077 0.255 936 Planarity : 0.023 0.230 1158 Dihedral : 18.616 119.879 2715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 4.95 % Favored : 94.14 % 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: -1.94 (0.27), residues: 780 helix: -1.30 (0.19), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.011 TRP B 187 HIS 0.011 0.006 HIS C 215 PHE 0.035 0.008 PHE B 243 TYR 0.044 0.009 TYR A 150 ARG 0.016 0.003 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.767 Fit side-chains REVERT: A 207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm) REVERT: A 230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp) REVERT: B 207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm) REVERT: C 207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.4141 time to fit residues: 117.3884 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7203 Z= 0.300 Angle : 0.974 11.623 9630 Z= 0.508 Chirality : 0.058 0.485 936 Planarity : 0.011 0.112 1158 Dihedral : 19.500 106.056 1334 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.48 % Favored : 94.99 % Rotamer: Outliers : 1.95 % Allowed : 7.66 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.28), residues: 780 helix: -0.68 (0.20), residues: 549 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP B 138 HIS 0.017 0.004 HIS C 215 PHE 0.103 0.006 PHE C 134 TYR 0.109 0.005 TYR B 155 ARG 0.029 0.002 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.762 Fit side-chains REVERT: A 87 ASP cc_start: 0.8444 (t70) cc_final: 0.8090 (t70) REVERT: A 207 ILE cc_start: 0.6976 (mt) cc_final: 0.6752 (mm) REVERT: A 248 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 207 ILE cc_start: 0.7140 (mt) cc_final: 0.6900 (mm) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 1.3483 time to fit residues: 117.8976 Evaluate side-chains 66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7203 Z= 0.237 Angle : 0.600 5.970 9630 Z= 0.293 Chirality : 0.043 0.129 936 Planarity : 0.005 0.059 1158 Dihedral : 17.112 89.297 1332 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.65 % Allowed : 8.56 % Favored : 89.79 % 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: 1.07 (0.29), residues: 780 helix: 1.15 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.20 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 42 HIS 0.003 0.001 HIS C 125 PHE 0.017 0.002 PHE A 134 TYR 0.013 0.002 TYR C 81 ARG 0.003 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.797 Fit side-chains REVERT: A 87 ASP cc_start: 0.8546 (t70) cc_final: 0.8116 (t70) REVERT: A 207 ILE cc_start: 0.6912 (mt) cc_final: 0.6704 (mm) REVERT: B 207 ILE cc_start: 0.7003 (mt) cc_final: 0.6770 (mm) outliers start: 8 outliers final: 1 residues processed: 72 average time/residue: 1.3317 time to fit residues: 101.5838 Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7203 Z= 0.149 Angle : 0.504 6.691 9630 Z= 0.242 Chirality : 0.039 0.120 936 Planarity : 0.004 0.047 1158 Dihedral : 14.714 66.566 1332 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.20 % Allowed : 8.56 % Favored : 90.24 % 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: 2.33 (0.30), residues: 780 helix: 2.14 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.16 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 42 HIS 0.003 0.001 HIS B 125 PHE 0.016 0.001 PHE A 134 TYR 0.009 0.001 TYR B 222 ARG 0.006 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.687 Fit side-chains REVERT: A 87 ASP cc_start: 0.8496 (t70) cc_final: 0.8080 (t70) REVERT: B 80 MET cc_start: 0.8455 (mtm) cc_final: 0.8172 (mtp) REVERT: B 207 ILE cc_start: 0.6900 (mt) cc_final: 0.6676 (mm) REVERT: C 225 PHE cc_start: 0.8181 (m-80) cc_final: 0.7841 (m-10) REVERT: C 244 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7720 (mtp180) outliers start: 5 outliers final: 0 residues processed: 75 average time/residue: 1.2368 time to fit residues: 98.0480 Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.7645 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7203 Z= 0.277 Angle : 0.619 6.713 9630 Z= 0.293 Chirality : 0.044 0.132 936 Planarity : 0.005 0.042 1158 Dihedral : 15.190 59.895 1332 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.35 % Allowed : 9.46 % Favored : 89.19 % 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: 2.18 (0.29), residues: 780 helix: 2.01 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.002 0.001 HIS A 215 PHE 0.016 0.002 PHE A 134 TYR 0.013 0.002 TYR A 81 ARG 0.005 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.690 Fit side-chains REVERT: A 87 ASP cc_start: 0.8585 (t70) cc_final: 0.8209 (t70) outliers start: 6 outliers final: 1 residues processed: 70 average time/residue: 1.2548 time to fit residues: 93.0267 Evaluate side-chains 58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.6342 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7203 Z= 0.234 Angle : 0.575 6.645 9630 Z= 0.273 Chirality : 0.042 0.125 936 Planarity : 0.005 0.041 1158 Dihedral : 14.185 59.887 1332 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.35 % Allowed : 9.61 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.34 (0.29), residues: 780 helix: 2.13 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 42 HIS 0.002 0.001 HIS C 125 PHE 0.016 0.002 PHE A 134 TYR 0.011 0.002 TYR C 81 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.656 Fit side-chains REVERT: A 87 ASP cc_start: 0.8573 (t70) cc_final: 0.8175 (t70) REVERT: C 244 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7700 (mtp180) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 1.3038 time to fit residues: 92.5942 Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7203 Z= 0.194 Angle : 0.545 6.762 9630 Z= 0.257 Chirality : 0.040 0.122 936 Planarity : 0.005 0.039 1158 Dihedral : 13.329 59.267 1332 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.05 % Allowed : 9.91 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.55 (0.29), residues: 780 helix: 2.32 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.766 Fit side-chains REVERT: A 87 ASP cc_start: 0.8549 (t70) cc_final: 0.8176 (t70) REVERT: A 121 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6907 (tp) REVERT: C 244 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7568 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 1.3720 time to fit residues: 94.2012 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7203 Z= 0.244 Angle : 0.591 6.980 9630 Z= 0.279 Chirality : 0.042 0.128 936 Planarity : 0.005 0.040 1158 Dihedral : 13.688 59.424 1332 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.20 % Allowed : 9.46 % Favored : 89.34 % 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: 2.38 (0.29), residues: 780 helix: 2.18 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.17 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 102 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.002 PHE A 134 TYR 0.012 0.002 TYR A 81 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.796 Fit side-chains REVERT: A 87 ASP cc_start: 0.8579 (t70) cc_final: 0.8193 (t70) REVERT: C 244 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7604 (mtm-85) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 1.3589 time to fit residues: 91.8704 Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7203 Z= 0.169 Angle : 0.524 6.694 9630 Z= 0.248 Chirality : 0.039 0.119 936 Planarity : 0.005 0.039 1158 Dihedral : 12.871 59.656 1332 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.35 % Allowed : 9.01 % Favored : 89.64 % 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: 2.69 (0.30), residues: 780 helix: 2.44 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 102 HIS 0.002 0.001 HIS C 125 PHE 0.015 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.775 Fit side-chains REVERT: A 87 ASP cc_start: 0.8534 (t70) cc_final: 0.8158 (t70) REVERT: C 244 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7585 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.3731 time to fit residues: 87.0912 Evaluate side-chains 56 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7203 Z= 0.208 Angle : 0.558 6.837 9630 Z= 0.263 Chirality : 0.041 0.125 936 Planarity : 0.005 0.039 1158 Dihedral : 13.053 59.993 1332 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.05 % Allowed : 9.61 % Favored : 89.34 % 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: 2.59 (0.29), residues: 780 helix: 2.34 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.22 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 102 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.001 PHE A 134 TYR 0.011 0.001 TYR C 81 ARG 0.004 0.000 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.710 Fit side-chains REVERT: A 87 ASP cc_start: 0.8563 (t70) cc_final: 0.8186 (t70) REVERT: C 244 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7589 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.4645 time to fit residues: 93.0056 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.123455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100573 restraints weight = 31344.592| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.33 r_work: 0.3036 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7203 Z= 0.230 Angle : 0.580 7.051 9630 Z= 0.273 Chirality : 0.042 0.127 936 Planarity : 0.005 0.040 1158 Dihedral : 13.237 59.543 1332 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.20 % Allowed : 9.76 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.50 (0.29), residues: 780 helix: 2.27 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.22 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 102 HIS 0.002 0.001 HIS C 125 PHE 0.016 0.002 PHE A 134 TYR 0.011 0.002 TYR C 81 ARG 0.004 0.000 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.67 seconds wall clock time: 41 minutes 27.05 seconds (2487.05 seconds total)