Starting phenix.real_space_refine on Sun Jun 8 00:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmi_60248/06_2025/8zmi_60248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmi_60248/06_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_60248/06_2025/8zmi_60248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmi_60248/06_2025/8zmi_60248.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmi_60248/06_2025/8zmi_60248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmi_60248/06_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-5710/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: 8.82, per 1000 atoms: 0.96 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: 2.57 Conformation dependent library (CDL) restraints added in 823.6 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: 4.46 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: 3.97 Time building geometry restraints manager: 2.98 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: 2.660 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- 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 : 0.719 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: 0.2125 time to fit residues: 38.5643 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 : 0.726 ------------------------------------------------------------------------------- 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 = 0.047156 restraints weight = 52769.324| |-----------------------------------------------------------------------------| 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 : 0.820 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: 0.2072 time to fit residues: 24.7405 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 : 0.755 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.068969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.048963 restraints weight = 51520.503| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.06 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2555 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= 0.112 Angle : 0.551 7.185 14005 Z= 0.279 Chirality : 0.034 0.158 1678 Planarity : 0.004 0.056 1158 Dihedral : 23.588 178.593 3396 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.81 % Allowed : 11.97 % Favored : 87.22 % 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: 1.24 (0.27), residues: 397 sheet: -1.99 (0.60), residues: 74 loop : -0.76 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 102 HIS 0.008 0.001 HIS B 242 PHE 0.016 0.001 PHE B 142 TYR 0.018 0.002 TYR B 323 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 418) hydrogen bonds : angle 4.16491 ( 1086) covalent geometry : bond 0.00234 ( 9771) covalent geometry : angle 0.55139 (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 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9500 (mm110) cc_final: 0.9112 (mp10) REVERT: B 63 CYS cc_start: 0.9380 (m) cc_final: 0.8519 (t) REVERT: B 65 ASP cc_start: 0.8079 (p0) cc_final: 0.7838 (p0) REVERT: B 193 PHE cc_start: 0.9215 (m-80) cc_final: 0.8832 (m-80) REVERT: B 194 TYR cc_start: 0.9143 (m-80) cc_final: 0.8393 (m-80) REVERT: B 214 MET cc_start: 0.8509 (mmm) cc_final: 0.8133 (mmm) REVERT: B 242 HIS cc_start: 0.7909 (t-170) cc_final: 0.7546 (t-170) REVERT: B 297 TYR cc_start: 0.9115 (m-10) cc_final: 0.8504 (m-10) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.1768 time to fit residues: 22.2097 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 : 0.954 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 199 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.065745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.045792 restraints weight = 52808.797| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.97 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9771 Z= 0.197 Angle : 0.598 7.753 14005 Z= 0.303 Chirality : 0.035 0.164 1678 Planarity : 0.005 0.057 1158 Dihedral : 23.768 179.257 3396 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.10 % Allowed : 13.43 % Favored : 84.47 % 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: 0.17 (0.33), residues: 694 helix: 1.05 (0.27), residues: 401 sheet: -2.29 (0.59), residues: 73 loop : -0.59 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 157 HIS 0.005 0.002 HIS A 242 PHE 0.012 0.002 PHE B 142 TYR 0.022 0.002 TYR B 123 ARG 0.003 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 418) hydrogen bonds : angle 4.31942 ( 1086) covalent geometry : bond 0.00404 ( 9771) covalent geometry : angle 0.59832 (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 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9545 (mm110) cc_final: 0.9192 (mp10) REVERT: B 63 CYS cc_start: 0.9502 (m) cc_final: 0.8537 (t) REVERT: B 65 ASP cc_start: 0.7944 (p0) cc_final: 0.7701 (p0) REVERT: B 193 PHE cc_start: 0.9306 (m-80) cc_final: 0.8897 (m-80) REVERT: B 194 TYR cc_start: 0.9149 (m-10) cc_final: 0.8383 (m-80) REVERT: B 226 TYR cc_start: 0.9013 (t80) cc_final: 0.8651 (t80) REVERT: B 297 TYR cc_start: 0.9109 (m-10) cc_final: 0.8497 (m-80) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.1655 time to fit residues: 17.9138 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 237 ILE 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 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: 3.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.067692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.047791 restraints weight = 52154.525| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.08 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3264 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= 0.109 Angle : 0.541 7.995 14005 Z= 0.272 Chirality : 0.033 0.159 1678 Planarity : 0.004 0.061 1158 Dihedral : 23.607 178.345 3396 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 14.40 % Favored : 83.98 % 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: 0.29 (0.33), residues: 694 helix: 1.20 (0.27), residues: 397 sheet: -2.04 (0.60), residues: 75 loop : -0.69 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 102 HIS 0.008 0.002 HIS A 358 PHE 0.007 0.001 PHE A 193 TYR 0.022 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 4.09319 ( 1086) covalent geometry : bond 0.00230 ( 9771) covalent geometry : angle 0.54106 (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 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9540 (mm110) cc_final: 0.9177 (mp10) REVERT: B 193 PHE cc_start: 0.9210 (m-80) cc_final: 0.8781 (m-80) REVERT: B 194 TYR cc_start: 0.9166 (m-10) cc_final: 0.8435 (m-80) REVERT: B 226 TYR cc_start: 0.8959 (t80) cc_final: 0.8666 (t80) REVERT: B 297 TYR cc_start: 0.9145 (m-10) cc_final: 0.8493 (m-10) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.1600 time to fit residues: 18.1938 Evaluate side-chains 66 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 366 LYS Chi-restraints excluded: chain B residue 178 ILE 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: 0.6980 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 0.0050 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 248 GLN A 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.068534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.049043 restraints weight = 50877.808| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.98 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3475 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= 0.101 Angle : 0.536 8.835 14005 Z= 0.266 Chirality : 0.033 0.173 1678 Planarity : 0.004 0.062 1158 Dihedral : 23.413 177.026 3396 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 15.53 % 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 (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: 0.38 (0.33), residues: 694 helix: 1.28 (0.27), residues: 404 sheet: -2.22 (0.59), residues: 82 loop : -0.55 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.006 0.001 HIS A 358 PHE 0.004 0.001 PHE A 103 TYR 0.020 0.002 TYR B 64 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 418) hydrogen bonds : angle 3.95982 ( 1086) covalent geometry : bond 0.00213 ( 9771) covalent geometry : angle 0.53600 (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 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9531 (mm110) cc_final: 0.9167 (mp10) REVERT: B 63 CYS cc_start: 0.9564 (m) cc_final: 0.8439 (t) REVERT: B 193 PHE cc_start: 0.9256 (m-80) cc_final: 0.8864 (m-80) REVERT: B 194 TYR cc_start: 0.9227 (m-10) cc_final: 0.8578 (m-80) REVERT: B 226 TYR cc_start: 0.8957 (t80) cc_final: 0.8699 (t80) REVERT: B 254 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5502 (tpt) REVERT: B 297 TYR cc_start: 0.9100 (m-10) cc_final: 0.8483 (m-10) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.1812 time to fit residues: 20.7206 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.067852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.048139 restraints weight = 52301.577| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 5.02 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3711 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= 0.114 Angle : 0.533 9.270 14005 Z= 0.268 Chirality : 0.033 0.169 1678 Planarity : 0.004 0.065 1158 Dihedral : 23.400 177.695 3396 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.78 % Allowed : 16.34 % Favored : 81.88 % 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: 1.26 (0.27), residues: 402 sheet: -2.38 (0.57), residues: 81 loop : -0.52 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS B 242 PHE 0.014 0.001 PHE B 142 TYR 0.018 0.002 TYR B 64 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 418) hydrogen bonds : angle 3.97531 ( 1086) covalent geometry : bond 0.00240 ( 9771) covalent geometry : angle 0.53336 (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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9533 (mm110) cc_final: 0.9157 (mp10) REVERT: B 80 MET cc_start: 0.9421 (mmm) cc_final: 0.9141 (mmm) REVERT: B 193 PHE cc_start: 0.9253 (m-80) cc_final: 0.8869 (m-80) REVERT: B 194 TYR cc_start: 0.9200 (m-10) cc_final: 0.8556 (m-80) REVERT: B 226 TYR cc_start: 0.9042 (t80) cc_final: 0.8693 (t80) REVERT: B 254 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5725 (tpt) REVERT: B 324 GLU cc_start: 0.9396 (mp0) cc_final: 0.9124 (pm20) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.2776 time to fit residues: 29.0072 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET 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: 0.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.068635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.049228 restraints weight = 52377.953| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.07 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3841 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= 0.104 Angle : 0.539 9.455 14005 Z= 0.269 Chirality : 0.033 0.158 1678 Planarity : 0.004 0.067 1158 Dihedral : 23.322 176.317 3396 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.94 % Allowed : 15.86 % Favored : 82.20 % 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: 0.37 (0.33), residues: 694 helix: 1.25 (0.27), residues: 403 sheet: -2.17 (0.57), residues: 83 loop : -0.53 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 242 PHE 0.011 0.001 PHE B 142 TYR 0.017 0.001 TYR B 64 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 418) hydrogen bonds : angle 3.92335 ( 1086) covalent geometry : bond 0.00219 ( 9771) covalent geometry : angle 0.53852 (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 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9538 (mm110) cc_final: 0.9157 (mt0) REVERT: B 73 MET cc_start: 0.8403 (ppp) cc_final: 0.7998 (ppp) REVERT: B 192 ILE cc_start: 0.9333 (mp) cc_final: 0.9124 (mp) REVERT: B 193 PHE cc_start: 0.9248 (m-80) cc_final: 0.8801 (m-80) REVERT: B 194 TYR cc_start: 0.9226 (m-10) cc_final: 0.8560 (m-80) REVERT: B 226 TYR cc_start: 0.9011 (t80) cc_final: 0.8701 (t80) REVERT: B 252 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8883 (mp0) REVERT: B 254 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5692 (tpt) REVERT: B 297 TYR cc_start: 0.9091 (m-10) cc_final: 0.8502 (m-80) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.2106 time to fit residues: 23.9266 Evaluate side-chains 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 298 LEU 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: 0.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.068721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.049261 restraints weight = 51835.389| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 5.14 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9771 Z= 0.112 Angle : 0.545 10.244 14005 Z= 0.272 Chirality : 0.033 0.161 1678 Planarity : 0.004 0.070 1158 Dihedral : 23.305 176.808 3396 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.78 % Allowed : 16.34 % Favored : 81.88 % 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: 0.33 (0.33), residues: 694 helix: 1.37 (0.27), residues: 398 sheet: -2.59 (0.54), residues: 83 loop : -0.64 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS B 242 PHE 0.016 0.001 PHE A 193 TYR 0.009 0.001 TYR B 156 ARG 0.002 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 418) hydrogen bonds : angle 3.89162 ( 1086) covalent geometry : bond 0.00242 ( 9771) covalent geometry : angle 0.54524 (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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8635 (p90) REVERT: A 77 GLN cc_start: 0.9530 (mm110) cc_final: 0.9137 (mt0) REVERT: B 73 MET cc_start: 0.8457 (ppp) cc_final: 0.8140 (ppp) REVERT: B 193 PHE cc_start: 0.9178 (m-80) cc_final: 0.8629 (m-80) REVERT: B 226 TYR cc_start: 0.9013 (t80) cc_final: 0.8681 (t80) REVERT: B 243 MET cc_start: 0.8464 (mmt) cc_final: 0.8257 (mmp) REVERT: B 252 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8916 (mp0) REVERT: B 254 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5735 (tpt) REVERT: B 324 GLU cc_start: 0.9352 (mp0) cc_final: 0.9116 (pm20) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1877 time to fit residues: 19.5791 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 298 LEU 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: 10.0000 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.064720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045523 restraints weight = 53888.764| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.07 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9771 Z= 0.186 Angle : 0.623 10.498 14005 Z= 0.311 Chirality : 0.035 0.209 1678 Planarity : 0.005 0.071 1158 Dihedral : 23.743 175.993 3396 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.46 % Allowed : 17.15 % 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: 0.36 (0.33), residues: 694 helix: 1.14 (0.27), residues: 404 sheet: -1.83 (0.65), residues: 66 loop : -0.62 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 128 HIS 0.005 0.001 HIS B 358 PHE 0.026 0.002 PHE A 193 TYR 0.011 0.002 TYR B 323 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 418) hydrogen bonds : angle 4.21610 ( 1086) covalent geometry : bond 0.00388 ( 9771) covalent geometry : angle 0.62319 (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 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.797 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: 0.9573 (mm110) cc_final: 0.9173 (mt0) REVERT: B 193 PHE cc_start: 0.9249 (m-80) cc_final: 0.8705 (m-80) REVERT: B 194 TYR cc_start: 0.9143 (m-10) cc_final: 0.8627 (m-80) REVERT: B 197 MET cc_start: 0.9296 (mtm) cc_final: 0.8646 (pmm) REVERT: B 226 TYR cc_start: 0.9122 (t80) cc_final: 0.8773 (t80) REVERT: B 254 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.4267 (tpt) REVERT: B 324 GLU cc_start: 0.9408 (mp0) cc_final: 0.9164 (pm20) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.1817 time to fit residues: 17.7667 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 358 HIS Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET 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: 10.0000 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.066644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.047265 restraints weight = 53088.114| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.99 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9771 Z= 0.116 Angle : 0.574 10.398 14005 Z= 0.284 Chirality : 0.033 0.184 1678 Planarity : 0.004 0.072 1158 Dihedral : 23.488 174.110 3396 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.78 % Allowed : 17.31 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.33), residues: 694 helix: 1.44 (0.27), residues: 390 sheet: -1.94 (0.63), residues: 66 loop : -0.85 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 128 HIS 0.005 0.001 HIS B 242 PHE 0.016 0.001 PHE A 193 TYR 0.016 0.002 TYR B 64 ARG 0.003 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 418) hydrogen bonds : angle 3.98739 ( 1086) covalent geometry : bond 0.00253 ( 9771) covalent geometry : angle 0.57418 (14005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.27 seconds wall clock time: 86 minutes 7.48 seconds (5167.48 seconds total)