Starting phenix.real_space_refine on Sat Aug 23 02:19:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2025/8zmi_60248.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 171 5.49 5 S 40 5.16 5 C 5188 2.51 5 N 1598 2.21 5 O 2238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9235 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 3594 Classifications: {'RNA': 169} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 80, 'rna3p_pyr': 73} Link IDs: {'rna2p': 16, 'rna3p': 152} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.30 Number of scatterers: 9235 At special positions: 0 Unit cell: (89.38, 116.44, 138.58, 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 40 16.00 P 171 15.00 O 2238 8.00 N 1598 7.00 C 5188 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=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 246.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 63.6% alpha, 6.4% beta 51 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.618A pdb=" N MET A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 112 removed outlier: 3.714A pdb=" N GLY A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 152 through 167 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 189 through 206 Proline residue: A 195 - end of helix removed outlier: 3.813A pdb=" N ILE A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 289 through 304 removed outlier: 4.616A pdb=" N LEU A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 336 through 362 Proline residue: A 342 - end of helix Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 74 through 92 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 108 through 112 removed outlier: 4.277A pdb=" N GLY B 111 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 132 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 189 through 205 Proline residue: B 195 - end of helix removed outlier: 3.955A pdb=" N ILE B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 289 through 304 removed outlier: 4.661A pdb=" N LEU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.573A pdb=" N GLY B 315 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 336 through 362 Proline residue: B 342 - end of helix Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.670A pdb=" N GLU A 44 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 64 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 211 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 66 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 63 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 98 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 65 " --> pdb=" O TRP A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.559A pdb=" N LYS A 318 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.899A pdb=" N GLU B 44 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE B 238 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS B 210 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 6.864A pdb=" N ASP B 65 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 306 through 308 292 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 3328 1.45 - 1.57: 4668 1.57 - 1.69: 341 1.69 - 1.81: 60 Bond restraints: 9771 Sorted by residual: bond pdb=" N ILE B 192 " pdb=" CA ILE B 192 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.08e-02 8.57e+03 9.92e+00 bond pdb=" N ASP B 185 " pdb=" CA ASP B 185 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.27e-02 6.20e+03 9.46e+00 bond pdb=" N ILE B 178 " pdb=" CA ILE B 178 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" N CYS B 175 " pdb=" CA CYS B 175 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 7.85e+00 bond pdb=" N GLU B 186 " pdb=" CA GLU B 186 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.34e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 13702 1.89 - 3.78: 255 3.78 - 5.68: 43 5.68 - 7.57: 1 7.57 - 9.46: 4 Bond angle restraints: 14005 Sorted by residual: angle pdb=" N ILE B 192 " pdb=" CA ILE B 192 " pdb=" C ILE B 192 " ideal model delta sigma weight residual 113.42 104.22 9.20 1.17e+00 7.31e-01 6.18e+01 angle pdb=" N ASP A 229 " pdb=" CA ASP A 229 " pdb=" C ASP A 229 " ideal model delta sigma weight residual 113.50 105.33 8.17 1.23e+00 6.61e-01 4.41e+01 angle pdb=" N GLU B 183 " pdb=" CA GLU B 183 " pdb=" C GLU B 183 " ideal model delta sigma weight residual 111.28 106.51 4.77 1.09e+00 8.42e-01 1.92e+01 angle pdb=" CA THR B 188 " pdb=" C THR B 188 " pdb=" O THR B 188 " ideal model delta sigma weight residual 120.36 115.86 4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" CA LYS A 233 " pdb=" C LYS A 233 " pdb=" O LYS A 233 " ideal model delta sigma weight residual 121.81 117.18 4.63 1.18e+00 7.18e-01 1.54e+01 ... (remaining 14000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5597 35.03 - 70.06: 515 70.06 - 105.09: 70 105.09 - 140.13: 1 140.13 - 175.16: 5 Dihedral angle restraints: 6188 sinusoidal: 4150 harmonic: 2038 Sorted by residual: dihedral pdb=" O4' U C 67 " pdb=" C1' U C 67 " pdb=" N1 U C 67 " pdb=" C2 U C 67 " ideal model delta sinusoidal sigma weight residual 200.00 41.69 158.31 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual 200.00 42.20 157.80 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C C 68 " pdb=" C1' C C 68 " pdb=" N1 C C 68 " pdb=" C2 C C 68 " ideal model delta sinusoidal sigma weight residual 200.00 51.51 148.49 1 1.50e+01 4.44e-03 7.90e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1446 0.054 - 0.107: 190 0.107 - 0.161: 31 0.161 - 0.214: 8 0.214 - 0.268: 3 Chirality restraints: 1678 Sorted by residual: chirality pdb=" P G C 46 " pdb=" OP1 G C 46 " pdb=" OP2 G C 46 " pdb=" O5' G C 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR B 188 " pdb=" N THR B 188 " pdb=" C THR B 188 " pdb=" CB THR B 188 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLU B 183 " pdb=" N GLU B 183 " pdb=" C GLU B 183 " pdb=" CB GLU B 183 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1675 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 174 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C ARG B 174 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG B 174 " -0.022 2.00e-02 2.50e+03 pdb=" N CYS B 175 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 102 " -0.027 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 102 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 102 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 102 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 226 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C TYR A 226 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 226 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS A 227 " -0.018 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 419 2.70 - 3.25: 8866 3.25 - 3.80: 16921 3.80 - 4.35: 21009 4.35 - 4.90: 31102 Nonbonded interactions: 78317 Sorted by model distance: nonbonded pdb=" O LYS B 277 " pdb=" O2' U C 23 " model vdw 2.146 3.040 nonbonded pdb=" OD1 ASP B 101 " pdb=" OG SER B 145 " model vdw 2.178 3.040 nonbonded pdb=" O PRO B 282 " pdb=" OH TYR B 330 " model vdw 2.198 3.040 nonbonded pdb=" O GLY B 66 " pdb=" O3' ATP B 401 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 332 " pdb=" OE1 GLU A 334 " model vdw 2.223 3.040 ... (remaining 78312 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' selection = (chain 'B' and resid 31 through 379) } 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=0.00 max=1.00 mean=1.00 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: 3.760 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9771 Z= 0.194 Angle : 0.622 9.461 14005 Z= 0.361 Chirality : 0.041 0.268 1678 Planarity : 0.005 0.070 1158 Dihedral : 22.149 175.157 4868 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.12 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.33), residues: 694 helix: 1.16 (0.27), residues: 405 sheet: -1.70 (0.66), residues: 71 loop : -0.69 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.012 0.002 TYR B 123 PHE 0.015 0.002 PHE B 193 TRP 0.057 0.002 TRP B 102 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9771) covalent geometry : angle 0.62248 (14005) hydrogen bonds : bond 0.10096 ( 418) hydrogen bonds : angle 4.86581 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.5520 (p90) cc_final: 0.5229 (p90) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1040 time to fit residues: 18.9995 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.057596 restraints weight = 62615.117| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.49 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9771 Z= 0.127 Angle : 0.586 7.308 14005 Z= 0.298 Chirality : 0.035 0.148 1678 Planarity : 0.005 0.054 1158 Dihedral : 23.450 175.036 3396 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.81 % Allowed : 9.06 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.33), residues: 694 helix: 1.20 (0.27), residues: 402 sheet: -2.29 (0.59), residues: 80 loop : -0.52 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.023 0.003 TYR A 323 PHE 0.011 0.001 PHE A 103 TRP 0.026 0.001 TRP B 102 HIS 0.008 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9771) covalent geometry : angle 0.58611 (14005) hydrogen bonds : bond 0.04268 ( 418) hydrogen bonds : angle 4.35345 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9464 (mm110) cc_final: 0.9111 (mp10) REVERT: A 325 GLU cc_start: 0.9677 (pt0) cc_final: 0.9340 (pp20) REVERT: A 329 ASP cc_start: 0.9312 (m-30) cc_final: 0.9092 (m-30) REVERT: B 63 CYS cc_start: 0.9013 (m) cc_final: 0.8527 (t) REVERT: B 133 MET cc_start: 0.8579 (mtp) cc_final: 0.8338 (mtp) REVERT: B 194 TYR cc_start: 0.9089 (m-80) cc_final: 0.8480 (m-80) REVERT: B 217 ARG cc_start: 0.9181 (ptm-80) cc_final: 0.8848 (ttt-90) REVERT: B 226 TYR cc_start: 0.8954 (t80) cc_final: 0.8705 (t80) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.0852 time to fit residues: 11.7345 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.070416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050328 restraints weight = 51215.297| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.07 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9771 Z= 0.114 Angle : 0.541 6.951 14005 Z= 0.274 Chirality : 0.033 0.150 1678 Planarity : 0.004 0.055 1158 Dihedral : 23.360 178.212 3396 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.46 % Allowed : 12.14 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.33), residues: 694 helix: 1.17 (0.27), residues: 397 sheet: -1.96 (0.60), residues: 74 loop : -0.73 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 371 TYR 0.018 0.002 TYR B 123 PHE 0.009 0.001 PHE A 103 TRP 0.015 0.001 TRP B 102 HIS 0.008 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9771) covalent geometry : angle 0.54121 (14005) hydrogen bonds : bond 0.04025 ( 418) hydrogen bonds : angle 4.08721 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9458 (mm110) cc_final: 0.9106 (mp10) REVERT: A 268 GLU cc_start: 0.9323 (tp30) cc_final: 0.9116 (tp30) REVERT: A 325 GLU cc_start: 0.9660 (pt0) cc_final: 0.9346 (pp20) REVERT: A 329 ASP cc_start: 0.9231 (m-30) cc_final: 0.9006 (m-30) REVERT: B 63 CYS cc_start: 0.9358 (m) cc_final: 0.8508 (t) REVERT: B 65 ASP cc_start: 0.8029 (p0) cc_final: 0.7827 (p0) REVERT: B 80 MET cc_start: 0.9450 (mmm) cc_final: 0.9243 (mmm) REVERT: B 193 PHE cc_start: 0.9233 (m-80) cc_final: 0.8723 (m-80) REVERT: B 194 TYR cc_start: 0.9133 (m-80) cc_final: 0.8374 (m-80) REVERT: B 226 TYR cc_start: 0.9070 (t80) cc_final: 0.8825 (t80) REVERT: B 242 HIS cc_start: 0.7797 (t-170) cc_final: 0.7526 (t-170) REVERT: B 297 TYR cc_start: 0.9064 (m-10) cc_final: 0.8560 (m-10) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.0709 time to fit residues: 9.4578 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.066907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046883 restraints weight = 52664.004| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 5.02 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9771 Z= 0.160 Angle : 0.572 7.655 14005 Z= 0.290 Chirality : 0.034 0.159 1678 Planarity : 0.004 0.056 1158 Dihedral : 23.605 179.458 3396 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.10 % Allowed : 13.27 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.33), residues: 694 helix: 1.15 (0.27), residues: 401 sheet: -2.26 (0.63), residues: 63 loop : -0.72 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.022 0.002 TYR B 123 PHE 0.011 0.001 PHE B 193 TRP 0.010 0.001 TRP B 102 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9771) covalent geometry : angle 0.57214 (14005) hydrogen bonds : bond 0.04376 ( 418) hydrogen bonds : angle 4.14668 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9517 (mm110) cc_final: 0.9176 (mp10) REVERT: A 268 GLU cc_start: 0.9372 (tp30) cc_final: 0.9166 (tp30) REVERT: B 63 CYS cc_start: 0.9496 (m) cc_final: 0.8574 (t) REVERT: B 65 ASP cc_start: 0.7781 (p0) cc_final: 0.7562 (p0) REVERT: B 193 PHE cc_start: 0.9298 (m-80) cc_final: 0.8783 (m-80) REVERT: B 226 TYR cc_start: 0.9160 (t80) cc_final: 0.8866 (t80) REVERT: B 297 TYR cc_start: 0.9152 (m-10) cc_final: 0.8689 (m-80) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.0836 time to fit residues: 10.5042 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.067979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048335 restraints weight = 52171.884| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.93 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9771 Z= 0.124 Angle : 0.539 7.630 14005 Z= 0.271 Chirality : 0.033 0.156 1678 Planarity : 0.004 0.060 1158 Dihedral : 23.551 178.233 3396 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.27 % Allowed : 14.56 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.33), residues: 694 helix: 1.25 (0.27), residues: 404 sheet: -2.31 (0.63), residues: 62 loop : -0.66 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.020 0.002 TYR B 123 PHE 0.014 0.001 PHE A 193 TRP 0.009 0.001 TRP A 102 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9771) covalent geometry : angle 0.53871 (14005) hydrogen bonds : bond 0.03967 ( 418) hydrogen bonds : angle 4.03265 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9514 (mm110) cc_final: 0.9171 (mp10) REVERT: A 268 GLU cc_start: 0.9386 (tp30) cc_final: 0.9182 (tp30) REVERT: A 325 GLU cc_start: 0.9654 (pt0) cc_final: 0.9317 (pp20) REVERT: A 329 ASP cc_start: 0.9260 (m-30) cc_final: 0.9040 (m-30) REVERT: B 193 PHE cc_start: 0.9198 (m-80) cc_final: 0.8734 (m-80) REVERT: B 194 TYR cc_start: 0.9167 (m-10) cc_final: 0.8470 (m-80) REVERT: B 226 TYR cc_start: 0.9129 (t80) cc_final: 0.8849 (t80) REVERT: B 243 MET cc_start: 0.8633 (tpp) cc_final: 0.8334 (tpp) REVERT: B 252 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8819 (mp0) REVERT: B 297 TYR cc_start: 0.9164 (m-10) cc_final: 0.8500 (m-10) REVERT: B 324 GLU cc_start: 0.9419 (mp0) cc_final: 0.9012 (pm20) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.0854 time to fit residues: 10.4110 Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.047723 restraints weight = 51735.391| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 5.03 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9771 Z= 0.123 Angle : 0.534 8.384 14005 Z= 0.267 Chirality : 0.032 0.159 1678 Planarity : 0.004 0.061 1158 Dihedral : 23.483 179.372 3396 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.10 % Allowed : 15.05 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.33), residues: 694 helix: 1.28 (0.27), residues: 402 sheet: -2.67 (0.55), residues: 81 loop : -0.46 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.020 0.002 TYR B 123 PHE 0.011 0.001 PHE A 193 TRP 0.010 0.001 TRP A 102 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9771) covalent geometry : angle 0.53393 (14005) hydrogen bonds : bond 0.03928 ( 418) hydrogen bonds : angle 3.98373 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9523 (mm110) cc_final: 0.9169 (mp10) REVERT: A 268 GLU cc_start: 0.9407 (tp30) cc_final: 0.9201 (tp30) REVERT: B 193 PHE cc_start: 0.9289 (m-80) cc_final: 0.8895 (m-80) REVERT: B 252 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8839 (mp0) REVERT: B 297 TYR cc_start: 0.9146 (m-10) cc_final: 0.8603 (m-80) outliers start: 13 outliers final: 12 residues processed: 79 average time/residue: 0.0860 time to fit residues: 10.1719 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 overall best weight: 1.8196 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.045892 restraints weight = 52983.705| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.08 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9771 Z= 0.161 Angle : 0.582 9.167 14005 Z= 0.291 Chirality : 0.034 0.171 1678 Planarity : 0.004 0.064 1158 Dihedral : 23.616 177.878 3396 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 15.21 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.33), residues: 694 helix: 1.29 (0.27), residues: 402 sheet: -2.09 (0.64), residues: 66 loop : -0.63 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.038 0.003 TYR B 226 PHE 0.010 0.001 PHE A 193 TRP 0.018 0.002 TRP B 128 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9771) covalent geometry : angle 0.58200 (14005) hydrogen bonds : bond 0.04394 ( 418) hydrogen bonds : angle 4.13506 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9539 (mm110) cc_final: 0.9153 (mt0) REVERT: B 193 PHE cc_start: 0.9317 (m-80) cc_final: 0.8935 (m-80) REVERT: B 194 TYR cc_start: 0.9189 (m-10) cc_final: 0.8493 (m-80) REVERT: B 226 TYR cc_start: 0.8848 (t80) cc_final: 0.8624 (t80) REVERT: B 252 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8894 (mp0) REVERT: B 324 GLU cc_start: 0.9376 (mp0) cc_final: 0.9119 (pm20) outliers start: 17 outliers final: 16 residues processed: 77 average time/residue: 0.0906 time to fit residues: 10.3239 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.072366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054395 restraints weight = 63297.265| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 5.26 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9771 Z= 0.110 Angle : 0.552 9.769 14005 Z= 0.276 Chirality : 0.033 0.169 1678 Planarity : 0.004 0.061 1158 Dihedral : 23.440 174.735 3396 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.94 % Allowed : 16.67 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.33), residues: 694 helix: 1.28 (0.27), residues: 400 sheet: -2.70 (0.55), residues: 81 loop : -0.49 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.033 0.002 TYR B 226 PHE 0.019 0.001 PHE A 193 TRP 0.011 0.001 TRP B 128 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9771) covalent geometry : angle 0.55239 (14005) hydrogen bonds : bond 0.03930 ( 418) hydrogen bonds : angle 4.03140 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9546 (mm110) cc_final: 0.9160 (mt0) REVERT: A 325 GLU cc_start: 0.9635 (pt0) cc_final: 0.9354 (pp20) REVERT: B 193 PHE cc_start: 0.9171 (m-80) cc_final: 0.8634 (m-80) REVERT: B 194 TYR cc_start: 0.9191 (m-10) cc_final: 0.8540 (m-80) REVERT: B 252 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8925 (mp0) REVERT: B 324 GLU cc_start: 0.9402 (mp0) cc_final: 0.9126 (pm20) outliers start: 12 outliers final: 12 residues processed: 72 average time/residue: 0.0844 time to fit residues: 9.2839 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.068361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.048998 restraints weight = 51873.880| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 5.10 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9771 Z= 0.110 Angle : 0.557 10.428 14005 Z= 0.276 Chirality : 0.033 0.168 1678 Planarity : 0.004 0.068 1158 Dihedral : 23.344 174.675 3396 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.75 % Allowed : 15.70 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.33), residues: 694 helix: 1.37 (0.27), residues: 399 sheet: -2.37 (0.57), residues: 83 loop : -0.61 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.018 0.002 TYR B 123 PHE 0.038 0.001 PHE B 35 TRP 0.010 0.001 TRP A 102 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9771) covalent geometry : angle 0.55691 (14005) hydrogen bonds : bond 0.03869 ( 418) hydrogen bonds : angle 4.01136 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9528 (mm110) cc_final: 0.9143 (mt0) REVERT: A 325 GLU cc_start: 0.9624 (pt0) cc_final: 0.9368 (pp20) REVERT: B 193 PHE cc_start: 0.9246 (m-80) cc_final: 0.8723 (m-80) REVERT: B 194 TYR cc_start: 0.9208 (m-10) cc_final: 0.8712 (m-80) REVERT: B 197 MET cc_start: 0.9131 (mtm) cc_final: 0.8661 (pmm) REVERT: B 226 TYR cc_start: 0.8412 (t80) cc_final: 0.8128 (t80) REVERT: B 252 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8866 (mp0) outliers start: 17 outliers final: 14 residues processed: 77 average time/residue: 0.0925 time to fit residues: 10.5613 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.067985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.048646 restraints weight = 52471.448| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 5.19 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9771 Z= 0.121 Angle : 0.567 11.034 14005 Z= 0.281 Chirality : 0.033 0.165 1678 Planarity : 0.004 0.071 1158 Dihedral : 23.359 174.766 3396 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.27 % Allowed : 16.67 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.34), residues: 694 helix: 1.41 (0.27), residues: 399 sheet: -2.72 (0.55), residues: 83 loop : -0.52 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.018 0.002 TYR B 64 PHE 0.015 0.001 PHE A 193 TRP 0.026 0.001 TRP B 128 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9771) covalent geometry : angle 0.56735 (14005) hydrogen bonds : bond 0.03900 ( 418) hydrogen bonds : angle 4.00800 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9672 (tt) cc_final: 0.9443 (pp) REVERT: A 77 GLN cc_start: 0.9529 (mm110) cc_final: 0.9154 (mt0) REVERT: A 325 GLU cc_start: 0.9636 (pt0) cc_final: 0.9359 (pp20) REVERT: B 193 PHE cc_start: 0.9240 (m-80) cc_final: 0.8699 (m-80) REVERT: B 194 TYR cc_start: 0.9197 (m-10) cc_final: 0.8690 (m-80) REVERT: B 197 MET cc_start: 0.9115 (mtm) cc_final: 0.8641 (pmm) REVERT: B 226 TYR cc_start: 0.8500 (t80) cc_final: 0.8130 (t80) REVERT: B 252 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8897 (mp0) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 0.0803 time to fit residues: 7.9804 Evaluate side-chains 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.069785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.051676 restraints weight = 63673.448| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 5.35 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9771 Z= 0.183 Angle : 0.609 10.692 14005 Z= 0.303 Chirality : 0.035 0.204 1678 Planarity : 0.004 0.069 1158 Dihedral : 23.560 174.918 3396 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.27 % Allowed : 16.67 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.33), residues: 694 helix: 1.48 (0.28), residues: 390 sheet: -1.99 (0.68), residues: 64 loop : -0.83 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.016 0.002 TYR B 64 PHE 0.024 0.002 PHE B 35 TRP 0.023 0.002 TRP B 128 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9771) covalent geometry : angle 0.60941 (14005) hydrogen bonds : bond 0.04416 ( 418) hydrogen bonds : angle 4.17782 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.83 seconds wall clock time: 40 minutes 6.66 seconds (2406.66 seconds total)