Starting phenix.real_space_refine on Mon May 12 15:57:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmi_60248/05_2025/8zmi_60248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmi_60248/05_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_60248/05_2025/8zmi_60248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmi_60248/05_2025/8zmi_60248.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmi_60248/05_2025/8zmi_60248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmi_60248/05_2025/8zmi_60248.cif" } resolution = 3.49 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.28, per 1000 atoms: 0.68 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: 2.24 Conformation dependent library (CDL) restraints added in 575.7 milliseconds 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: 3.80 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: 3.42 Time building geometry restraints manager: 2.60 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- 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 : 14.45 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 (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: 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 TRP 0.057 0.002 TRP B 102 HIS 0.004 0.001 HIS B 242 PHE 0.015 0.002 PHE B 193 TYR 0.012 0.002 TYR B 123 ARG 0.006 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.10096 ( 418) hydrogen bonds : angle 4.86581 ( 1086) covalent geometry : bond 0.00330 ( 9771) covalent geometry : angle 0.62248 (14005) *********************** 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 : 0.796 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: 0.2217 time to fit residues: 40.0100 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 : 0.823 ------------------------------------------------------------------------------- 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 70 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** A 314 ASN B 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.067278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.047155 restraints weight = 52769.326| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 5.08 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9771 Z= 0.204 Angle : 0.637 7.371 14005 Z= 0.326 Chirality : 0.036 0.148 1678 Planarity : 0.005 0.056 1158 Dihedral : 23.739 174.782 3396 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 9.39 % Favored : 89.32 % 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: 0.22 (0.33), residues: 694 helix: 1.10 (0.27), residues: 403 sheet: -2.16 (0.61), residues: 70 loop : -0.68 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 102 HIS 0.009 0.002 HIS A 242 PHE 0.013 0.002 PHE A 103 TYR 0.023 0.003 TYR A 323 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 418) hydrogen bonds : angle 4.52778 ( 1086) covalent geometry : bond 0.00424 ( 9771) covalent geometry : angle 0.63717 (14005) *********************** 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 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9523 (mm110) cc_final: 0.9186 (mp10) REVERT: B 63 CYS cc_start: 0.8975 (m) cc_final: 0.8626 (t) REVERT: B 194 TYR cc_start: 0.9126 (m-80) cc_final: 0.8485 (m-80) REVERT: B 214 MET cc_start: 0.8421 (mmm) cc_final: 0.7871 (mmm) REVERT: B 226 TYR cc_start: 0.9069 (t80) cc_final: 0.8764 (t80) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.2097 time to fit residues: 24.8719 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 35 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.069854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.049957 restraints weight = 51841.311| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.96 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9771 Z= 0.107 Angle : 0.548 6.960 14005 Z= 0.277 Chirality : 0.033 0.153 1678 Planarity : 0.004 0.056 1158 Dihedral : 23.524 179.140 3396 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.65 % Allowed : 12.46 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.33), residues: 694 helix: 1.23 (0.27), residues: 397 sheet: -1.95 (0.60), residues: 74 loop : -0.75 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.008 0.001 HIS B 242 PHE 0.016 0.001 PHE B 142 TYR 0.019 0.002 TYR B 323 ARG 0.004 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 418) hydrogen bonds : angle 4.12697 ( 1086) covalent geometry : bond 0.00224 ( 9771) covalent geometry : angle 0.54816 (14005) *********************** 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 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9493 (mm110) cc_final: 0.9117 (mp10) REVERT: B 63 CYS cc_start: 0.9366 (m) cc_final: 0.8515 (t) REVERT: B 65 ASP cc_start: 0.8013 (p0) cc_final: 0.7801 (p0) REVERT: B 80 MET cc_start: 0.9432 (mmm) cc_final: 0.9232 (mmm) REVERT: B 193 PHE cc_start: 0.9202 (m-80) cc_final: 0.8838 (m-80) REVERT: B 194 TYR cc_start: 0.9127 (m-80) cc_final: 0.8384 (m-80) REVERT: B 214 MET cc_start: 0.8556 (mmm) cc_final: 0.8179 (mmm) REVERT: B 242 HIS cc_start: 0.7864 (t-170) cc_final: 0.7640 (t-170) REVERT: B 297 TYR cc_start: 0.9090 (m-10) cc_final: 0.8514 (m-10) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.1537 time to fit residues: 19.1329 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.065078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.045174 restraints weight = 53561.706| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.96 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9771 Z= 0.219 Angle : 0.620 7.976 14005 Z= 0.314 Chirality : 0.035 0.168 1678 Planarity : 0.005 0.057 1158 Dihedral : 23.811 179.295 3396 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.43 % Allowed : 13.27 % Favored : 84.30 % 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: 0.12 (0.33), residues: 694 helix: 1.04 (0.27), residues: 401 sheet: -2.26 (0.60), residues: 73 loop : -0.70 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 157 HIS 0.006 0.002 HIS A 242 PHE 0.011 0.002 PHE A 35 TYR 0.022 0.002 TYR B 123 ARG 0.003 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 418) hydrogen bonds : angle 4.37899 ( 1086) covalent geometry : bond 0.00450 ( 9771) covalent geometry : angle 0.62014 (14005) *********************** 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 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9549 (mm110) cc_final: 0.9215 (mp10) REVERT: B 63 CYS cc_start: 0.9511 (m) cc_final: 0.8588 (t) REVERT: B 65 ASP cc_start: 0.7900 (p0) cc_final: 0.7655 (p0) REVERT: B 193 PHE cc_start: 0.9309 (m-80) cc_final: 0.8887 (m-80) REVERT: B 194 TYR cc_start: 0.9188 (m-10) cc_final: 0.8431 (m-80) REVERT: B 226 TYR cc_start: 0.9062 (t80) cc_final: 0.8748 (t80) REVERT: B 297 TYR cc_start: 0.9162 (m-10) cc_final: 0.8596 (m-10) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.2142 time to fit residues: 23.9572 Evaluate side-chains 66 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.0010 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.068322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.048709 restraints weight = 51622.105| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 5.03 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3413 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= 0.103 Angle : 0.532 7.594 14005 Z= 0.267 Chirality : 0.033 0.155 1678 Planarity : 0.004 0.060 1158 Dihedral : 23.542 177.108 3396 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.94 % Allowed : 14.89 % 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 (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: 0.39 (0.33), residues: 694 helix: 1.32 (0.27), residues: 399 sheet: -1.90 (0.61), residues: 74 loop : -0.81 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 102 HIS 0.003 0.001 HIS B 242 PHE 0.010 0.001 PHE A 320 TYR 0.020 0.002 TYR B 123 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 418) hydrogen bonds : angle 4.01749 ( 1086) covalent geometry : bond 0.00216 ( 9771) covalent geometry : angle 0.53156 (14005) *********************** 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 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9530 (mm110) cc_final: 0.9182 (mp10) REVERT: B 193 PHE cc_start: 0.9206 (m-80) cc_final: 0.8735 (m-80) REVERT: B 194 TYR cc_start: 0.9215 (m-10) cc_final: 0.8548 (m-80) REVERT: B 226 TYR cc_start: 0.8939 (t80) cc_final: 0.8650 (t80) REVERT: B 252 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8781 (mp0) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.1685 time to fit residues: 19.9707 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 366 LYS Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 298 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043841 restraints weight = 53720.709| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.02 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9771 Z= 0.211 Angle : 0.631 8.487 14005 Z= 0.318 Chirality : 0.035 0.177 1678 Planarity : 0.005 0.062 1158 Dihedral : 23.827 177.652 3396 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 16.02 % 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 (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: 0.25 (0.33), residues: 694 helix: 1.10 (0.27), residues: 404 sheet: -1.93 (0.65), residues: 66 loop : -0.75 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 128 HIS 0.004 0.002 HIS A 242 PHE 0.025 0.002 PHE B 35 TYR 0.024 0.002 TYR A 294 ARG 0.002 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 418) hydrogen bonds : angle 4.31174 ( 1086) covalent geometry : bond 0.00430 ( 9771) covalent geometry : angle 0.63104 (14005) *********************** 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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9559 (mm110) cc_final: 0.9191 (mp10) REVERT: B 193 PHE cc_start: 0.9235 (m-80) cc_final: 0.8935 (m-80) REVERT: B 194 TYR cc_start: 0.9177 (m-10) cc_final: 0.8432 (m-80) REVERT: B 226 TYR cc_start: 0.9162 (t80) cc_final: 0.8839 (t80) REVERT: B 252 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8840 (mp0) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 0.1703 time to fit residues: 17.3201 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.071245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.053055 restraints weight = 63553.959| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 5.33 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9771 Z= 0.117 Angle : 0.566 9.759 14005 Z= 0.282 Chirality : 0.033 0.163 1678 Planarity : 0.004 0.057 1158 Dihedral : 23.609 175.084 3396 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.94 % Allowed : 16.34 % Favored : 81.72 % 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: 0.28 (0.33), residues: 694 helix: 1.23 (0.27), residues: 397 sheet: -2.27 (0.58), residues: 75 loop : -0.68 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 102 HIS 0.003 0.001 HIS B 242 PHE 0.005 0.001 PHE A 103 TYR 0.019 0.002 TYR B 123 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 418) hydrogen bonds : angle 4.11142 ( 1086) covalent geometry : bond 0.00250 ( 9771) covalent geometry : angle 0.56647 (14005) *********************** 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 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9570 (mm110) cc_final: 0.9179 (mt0) REVERT: B 193 PHE cc_start: 0.9232 (m-80) cc_final: 0.8910 (m-80) REVERT: B 194 TYR cc_start: 0.9199 (m-10) cc_final: 0.8562 (m-80) REVERT: B 226 TYR cc_start: 0.9058 (t80) cc_final: 0.8805 (t80) REVERT: B 243 MET cc_start: 0.8405 (tpp) cc_final: 0.8189 (tpp) REVERT: B 252 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8880 (mp0) REVERT: B 297 TYR cc_start: 0.9046 (m-10) cc_final: 0.8600 (m-80) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 0.1646 time to fit residues: 17.8418 Evaluate side-chains 65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.066580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.046771 restraints weight = 53574.833| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 5.21 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9771 Z= 0.126 Angle : 0.565 9.922 14005 Z= 0.283 Chirality : 0.033 0.180 1678 Planarity : 0.004 0.067 1158 Dihedral : 23.539 175.184 3396 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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 (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: 0.31 (0.33), residues: 694 helix: 1.28 (0.27), residues: 396 sheet: -2.26 (0.58), residues: 75 loop : -0.70 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 128 HIS 0.002 0.001 HIS B 242 PHE 0.020 0.001 PHE B 35 TYR 0.019 0.001 TYR B 123 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 418) hydrogen bonds : angle 4.10544 ( 1086) covalent geometry : bond 0.00266 ( 9771) covalent geometry : angle 0.56526 (14005) *********************** 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 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9559 (mm110) cc_final: 0.9165 (mt0) REVERT: B 193 PHE cc_start: 0.9279 (m-80) cc_final: 0.8851 (m-80) REVERT: B 194 TYR cc_start: 0.9211 (m-10) cc_final: 0.8514 (m-80) REVERT: B 226 TYR cc_start: 0.9044 (t80) cc_final: 0.8760 (t80) REVERT: B 252 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8830 (mp0) REVERT: B 324 GLU cc_start: 0.9374 (mp0) cc_final: 0.9114 (pm20) outliers start: 12 outliers final: 11 residues processed: 63 average time/residue: 0.1629 time to fit residues: 15.7737 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 110 MET 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 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.065822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046047 restraints weight = 52955.623| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 5.10 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9771 Z= 0.152 Angle : 0.582 10.470 14005 Z= 0.291 Chirality : 0.034 0.185 1678 Planarity : 0.004 0.070 1158 Dihedral : 23.585 175.151 3396 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.94 % Allowed : 16.83 % Favored : 81.23 % 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: 0.46 (0.33), residues: 694 helix: 1.38 (0.27), residues: 390 sheet: -1.68 (0.66), residues: 66 loop : -0.82 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.003 0.001 HIS B 358 PHE 0.011 0.001 PHE A 193 TYR 0.017 0.002 TYR B 123 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 418) hydrogen bonds : angle 4.14116 ( 1086) covalent geometry : bond 0.00317 ( 9771) covalent geometry : angle 0.58237 (14005) *********************** 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 69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9560 (mm110) cc_final: 0.9169 (mt0) REVERT: B 80 MET cc_start: 0.9380 (mmm) cc_final: 0.9118 (mmm) REVERT: B 193 PHE cc_start: 0.9186 (m-80) cc_final: 0.8676 (m-80) REVERT: B 194 TYR cc_start: 0.9199 (m-10) cc_final: 0.8516 (m-80) REVERT: B 226 TYR cc_start: 0.9073 (t80) cc_final: 0.8765 (t80) REVERT: B 252 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8829 (mp0) REVERT: B 324 GLU cc_start: 0.9385 (mp0) cc_final: 0.9108 (pm20) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.1651 time to fit residues: 16.1368 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 110 MET 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 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.071645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053622 restraints weight = 63832.887| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.44 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9771 Z= 0.112 Angle : 0.564 10.916 14005 Z= 0.282 Chirality : 0.034 0.276 1678 Planarity : 0.004 0.071 1158 Dihedral : 23.426 174.355 3396 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.62 % Allowed : 17.64 % Favored : 80.74 % 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: 0.52 (0.33), residues: 694 helix: 1.34 (0.27), residues: 398 sheet: -1.72 (0.66), residues: 65 loop : -0.69 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 128 HIS 0.004 0.001 HIS B 242 PHE 0.037 0.001 PHE B 35 TYR 0.018 0.001 TYR B 123 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 418) hydrogen bonds : angle 4.02154 ( 1086) covalent geometry : bond 0.00242 ( 9771) covalent geometry : angle 0.56401 (14005) ********************** 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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9542 (mm110) cc_final: 0.9166 (mt0) REVERT: B 193 PHE cc_start: 0.9180 (m-80) cc_final: 0.8704 (m-80) REVERT: B 194 TYR cc_start: 0.9213 (m-10) cc_final: 0.8707 (m-80) REVERT: B 197 MET cc_start: 0.9156 (mtm) cc_final: 0.8635 (pmm) REVERT: B 226 TYR cc_start: 0.9019 (t80) cc_final: 0.8778 (t80) REVERT: B 252 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8833 (mp0) REVERT: B 324 GLU cc_start: 0.9399 (mp0) cc_final: 0.9123 (pm20) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1718 time to fit residues: 17.9408 Evaluate side-chains 65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain B residue 110 MET 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 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.071624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.053755 restraints weight = 63394.431| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 5.19 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9771 Z= 0.115 Angle : 0.566 11.193 14005 Z= 0.281 Chirality : 0.033 0.183 1678 Planarity : 0.004 0.071 1158 Dihedral : 23.369 174.725 3396 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.94 % Allowed : 17.48 % Favored : 80.58 % 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: 0.51 (0.33), residues: 694 helix: 1.36 (0.27), residues: 398 sheet: -2.01 (0.64), residues: 73 loop : -0.58 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.003 0.001 HIS B 74 PHE 0.007 0.001 PHE A 193 TYR 0.025 0.002 TYR B 123 ARG 0.002 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 418) hydrogen bonds : angle 3.99851 ( 1086) covalent geometry : bond 0.00248 ( 9771) covalent geometry : angle 0.56559 (14005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4312.24 seconds wall clock time: 75 minutes 58.11 seconds (4558.11 seconds total)