Starting phenix.real_space_refine on Tue Mar 3 12:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieb_35377/03_2026/8ieb_35377.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 2 5.49 5 S 35 5.16 5 C 2934 2.51 5 N 691 2.21 5 O 754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4416 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2062 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2250 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.25, per 1000 atoms: 0.28 Number of scatterers: 4416 At special positions: 0 Unit cell: (86.67, 87.48, 90.72, 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 35 16.00 P 2 15.00 O 754 8.00 N 691 7.00 C 2934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 197.2 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 76.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.540A pdb=" N ASN A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 151 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.645A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.848A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 284 through 317 Proline residue: A 310 - end of helix removed outlier: 3.660A pdb=" N ALA A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.543A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 150 removed outlier: 3.870A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.755A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.535A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 315 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.552A pdb=" N ARG B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 4.040A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 195 " --> pdb=" O MET A 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 201 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 193 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 190 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 631 1.32 - 1.44: 1203 1.44 - 1.57: 2620 1.57 - 1.70: 4 1.70 - 1.83: 50 Bond restraints: 4508 Sorted by residual: bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.318 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.430 1.380 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 4503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 6016 2.98 - 5.95: 81 5.95 - 8.93: 21 8.93 - 11.91: 1 11.91 - 14.89: 2 Bond angle restraints: 6121 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 108.78 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.52 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" C PRO A 252 " ideal model delta sigma weight residual 110.70 114.71 -4.01 1.22e+00 6.72e-01 1.08e+01 angle pdb=" C ASP A 109 " pdb=" N VAL A 110 " pdb=" CA VAL A 110 " ideal model delta sigma weight residual 121.70 127.56 -5.86 1.80e+00 3.09e-01 1.06e+01 angle pdb=" N PRO B 252 " pdb=" CA PRO B 252 " pdb=" C PRO B 252 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.05e+01 ... (remaining 6116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2358 17.13 - 34.27: 238 34.27 - 51.40: 51 51.40 - 68.54: 16 68.54 - 85.67: 7 Dihedral angle restraints: 2670 sinusoidal: 1062 harmonic: 1608 Sorted by residual: dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA MET B 82 " pdb=" C MET B 82 " pdb=" N SER B 83 " pdb=" CA SER B 83 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual 180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 575 0.051 - 0.102: 141 0.102 - 0.152: 37 0.152 - 0.203: 2 0.203 - 0.254: 2 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 260 " pdb=" CA ILE A 260 " pdb=" CG1 ILE A 260 " pdb=" CG2 ILE A 260 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 754 not shown) Planarity restraints: 709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 252 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 253 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 253 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 251 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 252 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.026 5.00e-02 4.00e+02 ... (remaining 706 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 336 2.74 - 3.28: 4383 3.28 - 3.82: 7448 3.82 - 4.36: 8174 4.36 - 4.90: 14626 Nonbonded interactions: 34967 Sorted by model distance: nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.198 3.040 nonbonded pdb=" O TYR B 146 " pdb=" OG1 THR B 150 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 182 " pdb=" OG1 THR A 186 " model vdw 2.271 3.040 nonbonded pdb=" O LEU B 274 " pdb=" OG1 THR B 278 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 114 " pdb=" OG SER A 114 " model vdw 2.331 3.040 ... (remaining 34962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 110 or resid 115 through 601)) selection = (chain 'B' and (resid 44 through 110 or resid 115 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB )) or resid 153 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 318 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.008 0.206 4510 Z= 0.370 Angle : 0.910 14.886 6125 Z= 0.418 Chirality : 0.049 0.254 757 Planarity : 0.007 0.069 709 Dihedral : 15.358 85.674 1624 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 548 helix: 1.21 (0.24), residues: 395 sheet: 1.82 (0.99), residues: 36 loop : -1.62 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 144 TYR 0.010 0.002 TYR A 280 PHE 0.023 0.002 PHE A 306 TRP 0.029 0.002 TRP A 229 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00781 ( 4508) covalent geometry : angle 0.90873 ( 6121) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.85695 ( 4) hydrogen bonds : bond 0.12687 ( 349) hydrogen bonds : angle 5.44429 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.160 Fit side-chains REVERT: A 199 MET cc_start: 0.6402 (ttm) cc_final: 0.6161 (ttm) REVERT: A 215 PHE cc_start: 0.7818 (p90) cc_final: 0.7361 (p90) REVERT: B 82 MET cc_start: 0.7560 (ttt) cc_final: 0.7343 (ttm) REVERT: B 96 CYS cc_start: 0.8471 (p) cc_final: 0.8271 (p) REVERT: B 122 THR cc_start: 0.8140 (t) cc_final: 0.7839 (p) REVERT: B 174 MET cc_start: 0.7415 (ttm) cc_final: 0.6914 (ttm) REVERT: B 215 PHE cc_start: 0.6930 (p90) cc_final: 0.6620 (p90) REVERT: B 216 CYS cc_start: 0.6227 (t) cc_final: 0.6016 (t) REVERT: B 222 ASP cc_start: 0.8256 (m-30) cc_final: 0.8008 (m-30) REVERT: B 261 MET cc_start: 0.8298 (mmm) cc_final: 0.8084 (mmp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0468 time to fit residues: 6.5551 Evaluate side-chains 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 311 GLN B 314 GLN B 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123612 restraints weight = 6187.919| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.16 r_work: 0.3545 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4510 Z= 0.174 Angle : 0.582 9.840 6125 Z= 0.303 Chirality : 0.042 0.187 757 Planarity : 0.005 0.042 709 Dihedral : 12.483 76.007 676 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.22 % Allowed : 9.76 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.36), residues: 548 helix: 2.21 (0.25), residues: 394 sheet: 2.63 (1.05), residues: 28 loop : -1.41 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.011 0.001 TYR A 280 PHE 0.018 0.001 PHE B 66 TRP 0.015 0.001 TRP A 229 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4508) covalent geometry : angle 0.58168 ( 6121) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.07472 ( 4) hydrogen bonds : bond 0.04762 ( 349) hydrogen bonds : angle 4.33554 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.191 Fit side-chains REVERT: A 199 MET cc_start: 0.6848 (ttm) cc_final: 0.6640 (ttm) REVERT: B 96 CYS cc_start: 0.8301 (p) cc_final: 0.8090 (p) REVERT: B 122 THR cc_start: 0.8314 (t) cc_final: 0.8108 (p) REVERT: B 150 THR cc_start: 0.8611 (p) cc_final: 0.8406 (p) REVERT: B 174 MET cc_start: 0.7979 (ttm) cc_final: 0.7515 (ttm) REVERT: B 187 ASP cc_start: 0.7448 (t0) cc_final: 0.7230 (t0) REVERT: B 216 CYS cc_start: 0.6011 (t) cc_final: 0.5767 (t) REVERT: B 222 ASP cc_start: 0.8380 (m-30) cc_final: 0.8153 (m-30) outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.0467 time to fit residues: 6.0082 Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.146175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123200 restraints weight = 6111.913| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.14 r_work: 0.3532 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4510 Z= 0.193 Angle : 0.571 8.132 6125 Z= 0.299 Chirality : 0.044 0.304 757 Planarity : 0.005 0.042 709 Dihedral : 11.844 73.536 676 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.42 % Allowed : 12.60 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.36), residues: 548 helix: 2.40 (0.25), residues: 393 sheet: 3.29 (1.29), residues: 14 loop : -1.44 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.015 0.001 TYR A 280 PHE 0.008 0.001 PHE B 215 TRP 0.013 0.001 TRP A 54 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 4508) covalent geometry : angle 0.57108 ( 6121) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.96121 ( 4) hydrogen bonds : bond 0.04724 ( 349) hydrogen bonds : angle 4.24209 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.153 Fit side-chains REVERT: A 199 MET cc_start: 0.6747 (ttm) cc_final: 0.6527 (ttm) REVERT: B 122 THR cc_start: 0.8297 (t) cc_final: 0.8080 (p) REVERT: B 174 MET cc_start: 0.8014 (ttm) cc_final: 0.7552 (ttm) REVERT: B 187 ASP cc_start: 0.7448 (t0) cc_final: 0.7187 (t0) REVERT: B 216 CYS cc_start: 0.5913 (t) cc_final: 0.5647 (t) REVERT: B 222 ASP cc_start: 0.8364 (m-30) cc_final: 0.7946 (m-30) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.0470 time to fit residues: 5.9784 Evaluate side-chains 89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.0170 chunk 46 optimal weight: 0.0020 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125771 restraints weight = 6098.433| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.09 r_work: 0.3580 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4510 Z= 0.119 Angle : 0.532 9.782 6125 Z= 0.275 Chirality : 0.040 0.290 757 Planarity : 0.004 0.043 709 Dihedral : 11.347 71.700 676 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 14.23 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.36), residues: 548 helix: 2.59 (0.24), residues: 393 sheet: 3.05 (1.30), residues: 14 loop : -1.35 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 123 TYR 0.011 0.001 TYR A 280 PHE 0.019 0.001 PHE B 66 TRP 0.014 0.001 TRP A 54 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4508) covalent geometry : angle 0.53192 ( 6121) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.92227 ( 4) hydrogen bonds : bond 0.04298 ( 349) hydrogen bonds : angle 4.07268 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7560 (tp) cc_final: 0.7341 (tt) REVERT: A 199 MET cc_start: 0.6715 (ttm) cc_final: 0.6452 (ttm) REVERT: A 318 PHE cc_start: 0.6853 (t80) cc_final: 0.6629 (t80) REVERT: B 116 MET cc_start: 0.6930 (tpp) cc_final: 0.6598 (mpp) REVERT: B 150 THR cc_start: 0.8587 (p) cc_final: 0.8366 (p) REVERT: B 174 MET cc_start: 0.7984 (ttm) cc_final: 0.7516 (ttm) REVERT: B 187 ASP cc_start: 0.7405 (t0) cc_final: 0.7169 (t0) REVERT: B 216 CYS cc_start: 0.5888 (t) cc_final: 0.5626 (t) outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 0.0433 time to fit residues: 5.9197 Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 6 optimal weight: 0.0270 chunk 46 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 53 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.149309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126289 restraints weight = 6249.100| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.22 r_work: 0.3581 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4510 Z= 0.114 Angle : 0.539 9.958 6125 Z= 0.274 Chirality : 0.040 0.281 757 Planarity : 0.004 0.042 709 Dihedral : 10.903 71.546 676 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.42 % Allowed : 16.26 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.36), residues: 548 helix: 2.67 (0.24), residues: 395 sheet: 2.80 (1.37), residues: 14 loop : -1.28 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.011 0.001 TYR A 280 PHE 0.012 0.001 PHE A 70 TRP 0.010 0.001 TRP A 54 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4508) covalent geometry : angle 0.53907 ( 6121) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.97046 ( 4) hydrogen bonds : bond 0.04156 ( 349) hydrogen bonds : angle 3.95568 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.155 Fit side-chains REVERT: A 199 MET cc_start: 0.6673 (ttm) cc_final: 0.6421 (ttm) REVERT: A 318 PHE cc_start: 0.6857 (t80) cc_final: 0.6645 (t80) REVERT: B 116 MET cc_start: 0.6858 (tpp) cc_final: 0.6530 (mpp) REVERT: B 125 SER cc_start: 0.8298 (t) cc_final: 0.7965 (p) REVERT: B 174 MET cc_start: 0.7990 (ttm) cc_final: 0.7536 (ttm) REVERT: B 187 ASP cc_start: 0.7452 (t0) cc_final: 0.7197 (t0) REVERT: B 216 CYS cc_start: 0.6066 (t) cc_final: 0.5847 (t) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.0444 time to fit residues: 5.9320 Evaluate side-chains 89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 18 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124195 restraints weight = 6303.918| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.12 r_work: 0.3555 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4510 Z= 0.159 Angle : 0.576 10.732 6125 Z= 0.294 Chirality : 0.043 0.333 757 Planarity : 0.004 0.043 709 Dihedral : 10.899 72.556 676 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.03 % Allowed : 16.06 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.36), residues: 548 helix: 2.64 (0.24), residues: 395 sheet: 3.12 (1.38), residues: 14 loop : -1.27 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.016 0.001 TYR A 280 PHE 0.008 0.001 PHE A 70 TRP 0.040 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4508) covalent geometry : angle 0.57531 ( 6121) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.96700 ( 4) hydrogen bonds : bond 0.04417 ( 349) hydrogen bonds : angle 3.96853 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6641 (ttm) cc_final: 0.6401 (ttm) REVERT: A 318 PHE cc_start: 0.6893 (t80) cc_final: 0.6661 (t80) REVERT: B 116 MET cc_start: 0.6919 (tpp) cc_final: 0.6634 (mpp) REVERT: B 174 MET cc_start: 0.7952 (ttm) cc_final: 0.7506 (ttm) REVERT: B 187 ASP cc_start: 0.7482 (t0) cc_final: 0.7180 (t0) REVERT: B 216 CYS cc_start: 0.6107 (t) cc_final: 0.5898 (t) REVERT: B 222 ASP cc_start: 0.8326 (m-30) cc_final: 0.7825 (m-30) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0449 time to fit residues: 5.9001 Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 49 optimal weight: 0.0970 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.146924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123514 restraints weight = 6287.933| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.19 r_work: 0.3542 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4510 Z= 0.154 Angle : 0.572 10.640 6125 Z= 0.293 Chirality : 0.043 0.321 757 Planarity : 0.004 0.042 709 Dihedral : 10.765 72.828 676 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 16.87 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.36), residues: 548 helix: 2.58 (0.24), residues: 395 sheet: 3.22 (1.37), residues: 14 loop : -1.24 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.013 0.001 TYR A 280 PHE 0.018 0.001 PHE B 275 TRP 0.056 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4508) covalent geometry : angle 0.57137 ( 6121) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.95147 ( 4) hydrogen bonds : bond 0.04421 ( 349) hydrogen bonds : angle 3.98722 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6609 (ttm) cc_final: 0.6384 (ttm) REVERT: A 318 PHE cc_start: 0.6918 (t80) cc_final: 0.6677 (t80) REVERT: B 116 MET cc_start: 0.6996 (tpp) cc_final: 0.6690 (mpp) REVERT: B 174 MET cc_start: 0.7989 (ttm) cc_final: 0.7549 (ttm) REVERT: B 187 ASP cc_start: 0.7457 (t0) cc_final: 0.7158 (t0) REVERT: B 222 ASP cc_start: 0.8299 (m-30) cc_final: 0.7841 (m-30) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.0479 time to fit residues: 6.4268 Evaluate side-chains 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124338 restraints weight = 6222.130| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.17 r_work: 0.3556 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4510 Z= 0.137 Angle : 0.584 11.369 6125 Z= 0.295 Chirality : 0.042 0.311 757 Planarity : 0.004 0.043 709 Dihedral : 10.478 72.411 676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 16.67 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.36), residues: 548 helix: 2.63 (0.24), residues: 395 sheet: 3.42 (1.38), residues: 14 loop : -1.16 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.012 0.001 TYR A 280 PHE 0.013 0.001 PHE A 70 TRP 0.055 0.002 TRP A 54 HIS 0.001 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4508) covalent geometry : angle 0.58305 ( 6121) SS BOND : bond 0.00136 ( 2) SS BOND : angle 1.32799 ( 4) hydrogen bonds : bond 0.04357 ( 349) hydrogen bonds : angle 3.97260 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.158 Fit side-chains REVERT: A 50 LEU cc_start: 0.6773 (tt) cc_final: 0.6550 (tp) REVERT: A 199 MET cc_start: 0.6577 (ttm) cc_final: 0.6346 (ttm) REVERT: A 318 PHE cc_start: 0.6922 (t80) cc_final: 0.6675 (t80) REVERT: B 116 MET cc_start: 0.6997 (tpp) cc_final: 0.6680 (mpp) REVERT: B 174 MET cc_start: 0.7968 (ttm) cc_final: 0.7533 (ttm) REVERT: B 187 ASP cc_start: 0.7487 (t0) cc_final: 0.7145 (t0) REVERT: B 222 ASP cc_start: 0.8277 (m-30) cc_final: 0.7798 (m-30) REVERT: B 261 MET cc_start: 0.7902 (mmm) cc_final: 0.7669 (mmp) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.0466 time to fit residues: 6.4524 Evaluate side-chains 95 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 overall best weight: 0.1458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125719 restraints weight = 6244.311| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.18 r_work: 0.3573 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4510 Z= 0.123 Angle : 0.593 11.795 6125 Z= 0.297 Chirality : 0.043 0.344 757 Planarity : 0.004 0.043 709 Dihedral : 10.298 71.839 676 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.42 % Allowed : 17.48 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.36), residues: 548 helix: 2.60 (0.24), residues: 395 sheet: 3.15 (1.02), residues: 24 loop : -1.18 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 123 TYR 0.012 0.001 TYR A 280 PHE 0.024 0.001 PHE B 66 TRP 0.081 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4508) covalent geometry : angle 0.59243 ( 6121) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.36705 ( 4) hydrogen bonds : bond 0.04251 ( 349) hydrogen bonds : angle 3.95065 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6532 (ttm) cc_final: 0.6304 (ttm) REVERT: A 318 PHE cc_start: 0.6939 (t80) cc_final: 0.6697 (t80) REVERT: B 116 MET cc_start: 0.7030 (tpp) cc_final: 0.6711 (mpp) REVERT: B 125 SER cc_start: 0.8292 (t) cc_final: 0.7934 (p) REVERT: B 174 MET cc_start: 0.7951 (ttm) cc_final: 0.7502 (ttm) REVERT: B 187 ASP cc_start: 0.7488 (t0) cc_final: 0.7168 (t0) REVERT: B 222 ASP cc_start: 0.8251 (m-30) cc_final: 0.7742 (m-30) REVERT: B 261 MET cc_start: 0.7907 (mmm) cc_final: 0.7677 (mmp) outliers start: 7 outliers final: 7 residues processed: 92 average time/residue: 0.0510 time to fit residues: 6.6307 Evaluate side-chains 92 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.123044 restraints weight = 6197.456| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.15 r_work: 0.3544 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4510 Z= 0.200 Angle : 0.663 13.234 6125 Z= 0.328 Chirality : 0.046 0.334 757 Planarity : 0.005 0.043 709 Dihedral : 10.494 74.489 676 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 17.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.36), residues: 548 helix: 2.51 (0.24), residues: 395 sheet: 3.23 (1.45), residues: 14 loop : -1.17 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.018 0.002 TYR A 280 PHE 0.014 0.001 PHE A 70 TRP 0.078 0.002 TRP A 54 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4508) covalent geometry : angle 0.66256 ( 6121) SS BOND : bond 0.00196 ( 2) SS BOND : angle 1.44481 ( 4) hydrogen bonds : bond 0.04732 ( 349) hydrogen bonds : angle 4.05340 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.6575 (ttm) cc_final: 0.6341 (ttm) REVERT: A 318 PHE cc_start: 0.6973 (t80) cc_final: 0.6689 (t80) REVERT: B 116 MET cc_start: 0.7116 (tpp) cc_final: 0.6768 (mpp) REVERT: B 174 MET cc_start: 0.8027 (ttm) cc_final: 0.7607 (ttm) REVERT: B 187 ASP cc_start: 0.7503 (t0) cc_final: 0.7170 (t0) REVERT: B 222 ASP cc_start: 0.8354 (m-30) cc_final: 0.7919 (m-30) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.0485 time to fit residues: 6.4989 Evaluate side-chains 92 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122451 restraints weight = 6238.732| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.06 r_work: 0.3538 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4510 Z= 0.247 Angle : 0.678 12.017 6125 Z= 0.343 Chirality : 0.049 0.400 757 Planarity : 0.005 0.043 709 Dihedral : 10.653 78.301 676 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.63 % Allowed : 18.09 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.36), residues: 548 helix: 2.32 (0.24), residues: 393 sheet: 3.27 (1.46), residues: 14 loop : -1.10 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.019 0.002 TYR A 280 PHE 0.013 0.001 PHE A 70 TRP 0.091 0.003 TRP A 54 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 4508) covalent geometry : angle 0.67730 ( 6121) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.43952 ( 4) hydrogen bonds : bond 0.04982 ( 349) hydrogen bonds : angle 4.14214 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.21 seconds wall clock time: 26 minutes 28.24 seconds (1588.24 seconds total)