Starting phenix.real_space_refine on Tue Mar 3 12:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nu5_49797/03_2026/9nu5_49797.map" } resolution = 3.7 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= 0.008 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2718 2.51 5 N 651 2.21 5 O 673 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: 4063 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3835 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain: "B" Number of atoms: 228 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 225 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY B 51 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 51 " occ=0.50 Time building chain proxies: 1.06, per 1000 atoms: 0.26 Number of scatterers: 4063 At special positions: 0 Unit cell: (63.7, 77.35, 76.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 673 8.00 N 651 7.00 C 2718 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: 0.27 Conformation dependent library (CDL) restraints added in 138.2 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid -1 through 32 removed outlier: 4.006A pdb=" N PHE A 5 " --> pdb=" O LYS A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 56 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 58 through 74 Proline residue: A 66 - end of helix removed outlier: 3.771A pdb=" N SER A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 105 Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.687A pdb=" N ASP A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.970A pdb=" N GLN A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 154 removed outlier: 4.214A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 178 removed outlier: 3.578A pdb=" N ALA A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 4.109A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 211 removed outlier: 4.013A pdb=" N ALA A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 257 Proline residue: A 235 - end of helix removed outlier: 3.524A pdb=" N LEU A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 297 removed outlier: 3.673A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 3.613A pdb=" N LEU A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 299 through 328 removed outlier: 3.643A pdb=" N ARG A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.734A pdb=" N PHE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 359 through 376 removed outlier: 4.362A pdb=" N GLY A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.508A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 406 through 432 removed outlier: 4.022A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 411 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 removed outlier: 3.969A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 499 removed outlier: 3.754A pdb=" N ARG A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.529A pdb=" N LEU B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.897A pdb=" N VAL B 55 " --> pdb=" O SER B 52 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 993 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: 0.69 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1216 1.34 - 1.46: 861 1.46 - 1.57: 2047 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4164 Sorted by residual: bond pdb=" CG1 ILE A 286 " pdb=" CD1 ILE A 286 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.71e+00 bond pdb=" C VAL A 43 " pdb=" O VAL A 43 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.12e-02 7.97e+03 1.40e+00 bond pdb=" CA LEU A 47 " pdb=" C LEU A 47 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.30e+00 bond pdb=" CG LEU A 205 " pdb=" CD1 LEU A 205 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CG LEU A 364 " pdb=" CD2 LEU A 364 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 ... (remaining 4159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 5349 1.25 - 2.50: 260 2.50 - 3.75: 39 3.75 - 5.01: 18 5.01 - 6.26: 13 Bond angle restraints: 5679 Sorted by residual: angle pdb=" C ARG A 53 " pdb=" N ILE A 54 " pdb=" CA ILE A 54 " ideal model delta sigma weight residual 120.74 117.01 3.73 1.43e+00 4.89e-01 6.80e+00 angle pdb=" CA TYR A 357 " pdb=" CB TYR A 357 " pdb=" CG TYR A 357 " ideal model delta sigma weight residual 113.90 118.51 -4.61 1.80e+00 3.09e-01 6.57e+00 angle pdb=" C ILE A 133 " pdb=" N THR A 134 " pdb=" CA THR A 134 " ideal model delta sigma weight residual 122.06 117.62 4.44 1.86e+00 2.89e-01 5.71e+00 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 112.75 115.84 -3.09 1.36e+00 5.41e-01 5.16e+00 angle pdb=" C LEU A 50 " pdb=" N LEU A 51 " pdb=" CA LEU A 51 " ideal model delta sigma weight residual 120.28 117.26 3.02 1.44e+00 4.82e-01 4.39e+00 ... (remaining 5674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.90: 2148 13.90 - 27.80: 210 27.80 - 41.70: 58 41.70 - 55.60: 8 55.60 - 69.50: 8 Dihedral angle restraints: 2432 sinusoidal: 894 harmonic: 1538 Sorted by residual: dihedral pdb=" CA ILE A 219 " pdb=" C ILE A 219 " pdb=" N ASN A 220 " pdb=" CA ASN A 220 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PRO A 184 " pdb=" C PRO A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASN A 183 " pdb=" C ASN A 183 " pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 449 0.039 - 0.077: 179 0.077 - 0.116: 49 0.116 - 0.154: 10 0.154 - 0.193: 2 Chirality restraints: 689 Sorted by residual: chirality pdb=" CA LEU A 205 " pdb=" N LEU A 205 " pdb=" C LEU A 205 " pdb=" CB LEU A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA PHE A 135 " pdb=" N PHE A 135 " pdb=" C PHE A 135 " pdb=" CB PHE A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CB VAL A 281 " pdb=" CA VAL A 281 " pdb=" CG1 VAL A 281 " pdb=" CG2 VAL A 281 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 686 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 330 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 331 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 234 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 235 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 201 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C LEU A 201 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A 201 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 202 " 0.008 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1083 2.79 - 3.32: 4271 3.32 - 3.85: 6733 3.85 - 4.37: 7784 4.37 - 4.90: 13144 Nonbonded interactions: 33015 Sorted by model distance: nonbonded pdb=" OG SER A 85 " pdb=" O LEU A 216 " model vdw 2.267 3.040 nonbonded pdb=" N TYR A -2 " pdb=" OE2 GLU A 302 " model vdw 2.286 3.120 nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 394 " model vdw 2.317 3.040 nonbonded pdb=" O VAL A 334 " pdb=" NH2 ARG A 477 " model vdw 2.385 3.120 nonbonded pdb=" O PHE A 45 " pdb=" ND2 ASN A 49 " model vdw 2.429 3.120 ... (remaining 33010 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.470 Find NCS groups from input model: 0.020 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.005 0.051 4164 Z= 0.201 Angle : 0.709 6.257 5679 Z= 0.369 Chirality : 0.044 0.193 689 Planarity : 0.005 0.038 687 Dihedral : 12.774 69.496 1444 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.52 (0.31), residues: 531 helix: -1.11 (0.19), residues: 443 sheet: None (None), residues: 0 loop : 0.81 (0.73), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 477 TYR 0.021 0.002 TYR A 357 PHE 0.022 0.002 PHE A 135 TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 4164) covalent geometry : angle 0.70868 ( 5679) hydrogen bonds : bond 0.11294 ( 334) hydrogen bonds : angle 5.09146 ( 993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7921 (tpt170) cc_final: 0.7554 (tpp-160) REVERT: A 218 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7650 (mtm-85) REVERT: A 329 SER cc_start: 0.8545 (p) cc_final: 0.8270 (p) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0651 time to fit residues: 9.0518 Evaluate side-chains 88 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120833 restraints weight = 13006.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125701 restraints weight = 4731.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128756 restraints weight = 2468.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130766 restraints weight = 1607.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131883 restraints weight = 1205.270| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4164 Z= 0.153 Angle : 0.629 6.189 5679 Z= 0.315 Chirality : 0.041 0.160 689 Planarity : 0.004 0.034 687 Dihedral : 4.992 57.880 569 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.48 % Allowed : 11.08 % Favored : 84.43 % 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: 1.12 (0.35), residues: 531 helix: 0.89 (0.23), residues: 450 sheet: None (None), residues: 0 loop : 0.49 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 477 TYR 0.021 0.002 TYR A 339 PHE 0.014 0.001 PHE A 162 TRP 0.011 0.001 TRP A 264 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4164) covalent geometry : angle 0.62885 ( 5679) hydrogen bonds : bond 0.05119 ( 334) hydrogen bonds : angle 4.11563 ( 993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 0 GLN cc_start: 0.7152 (mt0) cc_final: 0.6952 (mp10) REVERT: A 156 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7328 (tpp-160) REVERT: A 227 MET cc_start: 0.7674 (mmt) cc_final: 0.6888 (mmm) REVERT: A 257 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7701 (mt) REVERT: A 273 GLU cc_start: 0.8008 (tt0) cc_final: 0.7801 (tt0) REVERT: A 329 SER cc_start: 0.8620 (p) cc_final: 0.8257 (p) REVERT: A 339 TYR cc_start: 0.7669 (m-80) cc_final: 0.6960 (m-80) REVERT: A 477 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7152 (mtp180) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.0606 time to fit residues: 8.0403 Evaluate side-chains 96 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 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 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118322 restraints weight = 15488.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123410 restraints weight = 5232.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126705 restraints weight = 2646.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128796 restraints weight = 1687.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129848 restraints weight = 1247.970| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4164 Z= 0.148 Angle : 0.600 8.689 5679 Z= 0.299 Chirality : 0.039 0.144 689 Planarity : 0.004 0.032 687 Dihedral : 4.572 43.885 569 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.72 % Allowed : 14.62 % Favored : 80.66 % 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: 2.08 (0.36), residues: 531 helix: 1.63 (0.24), residues: 446 sheet: None (None), residues: 0 loop : 0.33 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 477 TYR 0.017 0.002 TYR B 36 PHE 0.010 0.001 PHE A 45 TRP 0.004 0.001 TRP A 154 HIS 0.010 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4164) covalent geometry : angle 0.59983 ( 5679) hydrogen bonds : bond 0.04640 ( 334) hydrogen bonds : angle 3.90967 ( 993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 0 GLN cc_start: 0.7167 (mt0) cc_final: 0.6944 (mp10) REVERT: A 227 MET cc_start: 0.7616 (mmt) cc_final: 0.6824 (mmm) REVERT: A 257 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 273 GLU cc_start: 0.8010 (tt0) cc_final: 0.7783 (tt0) REVERT: A 329 SER cc_start: 0.8633 (p) cc_final: 0.8313 (p) REVERT: A 339 TYR cc_start: 0.7593 (m-80) cc_final: 0.7256 (m-80) REVERT: A 446 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 482 MET cc_start: 0.7615 (mmt) cc_final: 0.7201 (mmt) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.0487 time to fit residues: 6.4176 Evaluate side-chains 99 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.142113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119809 restraints weight = 20212.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125311 restraints weight = 6126.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128894 restraints weight = 2925.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131118 restraints weight = 1784.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132564 restraints weight = 1285.488| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4164 Z= 0.126 Angle : 0.575 7.790 5679 Z= 0.283 Chirality : 0.038 0.144 689 Planarity : 0.004 0.030 687 Dihedral : 4.224 27.583 569 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.01 % Allowed : 16.98 % Favored : 79.01 % 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: 2.46 (0.36), residues: 531 helix: 1.95 (0.24), residues: 446 sheet: None (None), residues: 0 loop : 0.06 (0.69), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 477 TYR 0.016 0.002 TYR B 36 PHE 0.010 0.001 PHE A 45 TRP 0.007 0.001 TRP A 154 HIS 0.009 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4164) covalent geometry : angle 0.57513 ( 5679) hydrogen bonds : bond 0.04349 ( 334) hydrogen bonds : angle 3.73201 ( 993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.181 Fit side-chains REVERT: A 60 PHE cc_start: 0.9022 (t80) cc_final: 0.8808 (t80) REVERT: A 227 MET cc_start: 0.7473 (mmt) cc_final: 0.6733 (mmm) REVERT: A 273 GLU cc_start: 0.7973 (tt0) cc_final: 0.7755 (tt0) REVERT: A 329 SER cc_start: 0.8599 (p) cc_final: 0.8217 (p) REVERT: A 339 TYR cc_start: 0.7511 (m-80) cc_final: 0.7208 (m-80) REVERT: A 357 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8824 (m-10) REVERT: A 446 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 477 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7434 (mtp85) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 0.0506 time to fit residues: 6.7348 Evaluate side-chains 98 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.0010 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3744 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.142218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120455 restraints weight = 16588.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125672 restraints weight = 5512.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129075 restraints weight = 2750.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131245 restraints weight = 1720.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132525 restraints weight = 1252.372| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4164 Z= 0.129 Angle : 0.603 12.998 5679 Z= 0.290 Chirality : 0.038 0.140 689 Planarity : 0.004 0.031 687 Dihedral : 4.128 20.233 569 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.72 % Allowed : 18.63 % Favored : 76.65 % 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: 2.72 (0.36), residues: 531 helix: 2.13 (0.24), residues: 443 sheet: None (None), residues: 0 loop : 0.16 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 477 TYR 0.014 0.001 TYR B 36 PHE 0.009 0.001 PHE A 45 TRP 0.006 0.001 TRP A 154 HIS 0.005 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4164) covalent geometry : angle 0.60298 ( 5679) hydrogen bonds : bond 0.04260 ( 334) hydrogen bonds : angle 3.67501 ( 993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.7467 (mmt) cc_final: 0.6687 (mmm) REVERT: A 273 GLU cc_start: 0.7950 (tt0) cc_final: 0.7731 (tt0) REVERT: A 329 SER cc_start: 0.8612 (p) cc_final: 0.8256 (p) REVERT: A 355 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8951 (mp) REVERT: A 357 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8819 (m-10) REVERT: A 446 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 20 outliers final: 10 residues processed: 95 average time/residue: 0.0495 time to fit residues: 6.3996 Evaluate side-chains 96 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.138080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117446 restraints weight = 13123.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122165 restraints weight = 4860.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125261 restraints weight = 2561.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127205 restraints weight = 1658.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128469 restraints weight = 1240.225| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4164 Z= 0.172 Angle : 0.628 11.057 5679 Z= 0.306 Chirality : 0.040 0.148 689 Planarity : 0.004 0.033 687 Dihedral : 4.159 17.687 569 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.90 % Allowed : 17.69 % Favored : 76.42 % 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: 2.55 (0.36), residues: 531 helix: 2.07 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -0.16 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 477 TYR 0.012 0.002 TYR B 36 PHE 0.010 0.001 PHE A 274 TRP 0.007 0.001 TRP A 154 HIS 0.005 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4164) covalent geometry : angle 0.62778 ( 5679) hydrogen bonds : bond 0.04490 ( 334) hydrogen bonds : angle 3.74474 ( 993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.150 Fit side-chains REVERT: A 227 MET cc_start: 0.7600 (mmt) cc_final: 0.6850 (mmm) REVERT: A 257 LEU cc_start: 0.7753 (tt) cc_final: 0.7521 (tt) REVERT: A 273 GLU cc_start: 0.7943 (tt0) cc_final: 0.7738 (tt0) REVERT: A 329 SER cc_start: 0.8654 (p) cc_final: 0.8310 (p) REVERT: A 355 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 357 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: A 380 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 446 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8468 (mt) REVERT: A 477 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7471 (mtp180) outliers start: 25 outliers final: 18 residues processed: 99 average time/residue: 0.0503 time to fit residues: 6.7355 Evaluate side-chains 106 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.144644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122170 restraints weight = 19818.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127785 restraints weight = 6244.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131425 restraints weight = 2999.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133699 restraints weight = 1821.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135172 restraints weight = 1304.052| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4164 Z= 0.133 Angle : 0.608 9.830 5679 Z= 0.292 Chirality : 0.039 0.143 689 Planarity : 0.004 0.032 687 Dihedral : 4.101 17.659 569 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 5.19 % Allowed : 20.05 % Favored : 74.76 % 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: 2.63 (0.36), residues: 531 helix: 2.14 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.37 (0.71), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 477 TYR 0.012 0.001 TYR B 36 PHE 0.021 0.001 PHE A 60 TRP 0.007 0.001 TRP A 154 HIS 0.008 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4164) covalent geometry : angle 0.60774 ( 5679) hydrogen bonds : bond 0.04262 ( 334) hydrogen bonds : angle 3.64122 ( 993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.145 Fit side-chains REVERT: A 191 TRP cc_start: 0.8080 (m100) cc_final: 0.7856 (m100) REVERT: A 227 MET cc_start: 0.7489 (mmt) cc_final: 0.6721 (mmm) REVERT: A 257 LEU cc_start: 0.7669 (tt) cc_final: 0.6842 (mt) REVERT: A 273 GLU cc_start: 0.7908 (tt0) cc_final: 0.7673 (tt0) REVERT: A 329 SER cc_start: 0.8605 (p) cc_final: 0.8261 (p) REVERT: A 355 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 357 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8770 (m-10) REVERT: A 380 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 446 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8341 (mt) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.0513 time to fit residues: 6.6709 Evaluate side-chains 101 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.3246 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.145950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123265 restraints weight = 20725.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128977 restraints weight = 6457.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132705 restraints weight = 3071.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134906 restraints weight = 1851.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136467 restraints weight = 1330.706| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4164 Z= 0.126 Angle : 0.607 9.950 5679 Z= 0.290 Chirality : 0.039 0.144 689 Planarity : 0.004 0.033 687 Dihedral : 4.023 17.289 569 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.95 % Allowed : 20.52 % Favored : 74.53 % 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: 2.72 (0.36), residues: 531 helix: 2.18 (0.24), residues: 447 sheet: None (None), residues: 0 loop : -0.29 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.014 0.001 TYR A 339 PHE 0.022 0.001 PHE A 60 TRP 0.009 0.001 TRP A 154 HIS 0.008 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4164) covalent geometry : angle 0.60720 ( 5679) hydrogen bonds : bond 0.04123 ( 334) hydrogen bonds : angle 3.66619 ( 993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.164 Fit side-chains REVERT: A 191 TRP cc_start: 0.8056 (m100) cc_final: 0.7835 (m100) REVERT: A 227 MET cc_start: 0.7455 (mmt) cc_final: 0.6720 (mmm) REVERT: A 257 LEU cc_start: 0.7626 (tt) cc_final: 0.6827 (mt) REVERT: A 273 GLU cc_start: 0.7898 (tt0) cc_final: 0.7658 (tt0) REVERT: A 329 SER cc_start: 0.8547 (p) cc_final: 0.8195 (p) REVERT: A 355 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8971 (mp) REVERT: A 357 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8781 (m-10) REVERT: A 380 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 446 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 477 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7560 (mtm180) outliers start: 21 outliers final: 14 residues processed: 94 average time/residue: 0.0457 time to fit residues: 5.9846 Evaluate side-chains 103 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125049 restraints weight = 11402.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129729 restraints weight = 4523.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132664 restraints weight = 2432.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134615 restraints weight = 1615.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135458 restraints weight = 1199.794| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4164 Z= 0.142 Angle : 0.631 10.326 5679 Z= 0.299 Chirality : 0.039 0.142 689 Planarity : 0.004 0.033 687 Dihedral : 4.021 16.976 569 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 5.66 % Allowed : 19.81 % Favored : 74.53 % 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: 2.67 (0.36), residues: 531 helix: 2.17 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -0.42 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 477 TYR 0.013 0.002 TYR A 339 PHE 0.019 0.001 PHE A 60 TRP 0.008 0.001 TRP A 154 HIS 0.011 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4164) covalent geometry : angle 0.63085 ( 5679) hydrogen bonds : bond 0.04203 ( 334) hydrogen bonds : angle 3.67954 ( 993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.106 Fit side-chains REVERT: A 227 MET cc_start: 0.7463 (mmt) cc_final: 0.6762 (mmm) REVERT: A 265 MET cc_start: 0.8538 (mtp) cc_final: 0.8248 (mtp) REVERT: A 273 GLU cc_start: 0.7872 (tt0) cc_final: 0.7629 (tt0) REVERT: A 329 SER cc_start: 0.8570 (p) cc_final: 0.8227 (p) REVERT: A 355 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 357 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8765 (m-10) REVERT: A 380 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 446 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8365 (mt) REVERT: A 477 ARG cc_start: 0.7791 (mtm180) cc_final: 0.6807 (mtm-85) REVERT: A 480 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7661 (mtp85) outliers start: 24 outliers final: 15 residues processed: 99 average time/residue: 0.0479 time to fit residues: 6.4570 Evaluate side-chains 103 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122638 restraints weight = 16357.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127910 restraints weight = 5661.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131245 restraints weight = 2847.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133463 restraints weight = 1807.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134868 restraints weight = 1301.898| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4164 Z= 0.155 Angle : 0.654 10.777 5679 Z= 0.311 Chirality : 0.040 0.148 689 Planarity : 0.004 0.034 687 Dihedral : 4.107 16.964 569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.72 % Allowed : 20.52 % Favored : 74.76 % 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: 2.61 (0.36), residues: 531 helix: 2.14 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -0.49 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.015 0.002 TYR A 492 PHE 0.018 0.001 PHE A 60 TRP 0.008 0.001 TRP A 154 HIS 0.014 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4164) covalent geometry : angle 0.65427 ( 5679) hydrogen bonds : bond 0.04323 ( 334) hydrogen bonds : angle 3.78658 ( 993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.128 Fit side-chains REVERT: A 227 MET cc_start: 0.7480 (mmt) cc_final: 0.6730 (mmm) REVERT: A 265 MET cc_start: 0.8598 (mtp) cc_final: 0.8295 (mtp) REVERT: A 273 GLU cc_start: 0.7881 (tt0) cc_final: 0.7637 (tt0) REVERT: A 329 SER cc_start: 0.8547 (p) cc_final: 0.8222 (p) REVERT: A 355 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 357 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: A 380 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 446 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8385 (mt) REVERT: A 477 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7511 (mtm180) outliers start: 20 outliers final: 16 residues processed: 94 average time/residue: 0.0479 time to fit residues: 6.2615 Evaluate side-chains 102 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122901 restraints weight = 19897.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128496 restraints weight = 6360.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132090 restraints weight = 3069.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134365 restraints weight = 1868.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135755 restraints weight = 1336.183| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4164 Z= 0.142 Angle : 0.643 10.933 5679 Z= 0.306 Chirality : 0.039 0.157 689 Planarity : 0.004 0.033 687 Dihedral : 4.116 16.958 569 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.95 % Allowed : 20.28 % Favored : 74.76 % 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: 2.61 (0.36), residues: 531 helix: 2.16 (0.24), residues: 443 sheet: None (None), residues: 0 loop : -0.45 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 477 TYR 0.013 0.002 TYR A 339 PHE 0.026 0.001 PHE A 60 TRP 0.039 0.002 TRP A 154 HIS 0.014 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4164) covalent geometry : angle 0.64268 ( 5679) hydrogen bonds : bond 0.04267 ( 334) hydrogen bonds : angle 3.78229 ( 993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1044.12 seconds wall clock time: 18 minutes 41.02 seconds (1121.02 seconds total)