Starting phenix.real_space_refine on Thu Sep 10 20:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lii_4053/09_2026/5lii_4053.map" } resolution = 3.8 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= 0.270 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 11 5.16 5 C 1947 2.51 5 N 545 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3098 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 414} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 7, 'ASP:plan': 6, 'GLN:plan1': 9, 'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 0.95, per 1000 atoms: 0.31 Number of scatterers: 3098 At special positions: 0 Unit cell: (66.24, 100.74, 97.98, 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 11 16.00 O 595 8.00 N 545 7.00 C 1947 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: 0.28 Conformation dependent library (CDL) restraints added in 128.0 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 11.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 125 through 131 Processing helix chain 'P' and resid 137 through 159 removed outlier: 3.620A pdb=" N THR P 142 " --> pdb=" O SER P 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR P 159 " --> pdb=" O TRP P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 210 removed outlier: 3.528A pdb=" N ASN P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 70 through 72 removed outlier: 6.829A pdb=" N ARG P 71 " --> pdb=" O GLU P 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'P' and resid 325 through 326 removed outlier: 3.509A pdb=" N SER P 326 " --> pdb=" O ILE P 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'P' and resid 348 through 350 Processing sheet with id=AA5, first strand: chain 'P' and resid 404 through 407 41 hydrogen bonds defined for protein. 114 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: 0.41 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: 1.13 - 1.27: 542 1.27 - 1.41: 749 1.41 - 1.55: 1832 1.55 - 1.69: 3 1.69 - 1.83: 22 Bond restraints: 3148 Sorted by residual: bond pdb=" C ALA P 101 " pdb=" N PRO P 102 " ideal model delta sigma weight residual 1.334 1.134 0.200 2.34e-02 1.83e+03 7.32e+01 bond pdb=" CA MET P 409 " pdb=" CB MET P 409 " ideal model delta sigma weight residual 1.528 1.420 0.109 1.35e-02 5.49e+03 6.47e+01 bond pdb=" CB TYR P 441 " pdb=" CG TYR P 441 " ideal model delta sigma weight residual 1.512 1.445 0.067 2.20e-02 2.07e+03 9.31e+00 bond pdb=" CG LEU P 181 " pdb=" CD1 LEU P 181 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.04e+00 bond pdb=" CB PRO P 137 " pdb=" CG PRO P 137 " ideal model delta sigma weight residual 1.506 1.400 0.106 3.90e-02 6.57e+02 7.41e+00 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 4260 10.07 - 20.15: 20 20.15 - 30.22: 1 30.22 - 40.29: 3 40.29 - 50.37: 2 Bond angle restraints: 4286 Sorted by residual: angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" CB PRO P 399 " ideal model delta sigma weight residual 102.60 65.95 36.65 1.10e+00 8.26e-01 1.11e+03 angle pdb=" N VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta sigma weight residual 110.49 78.16 32.33 1.15e+00 7.56e-01 7.90e+02 angle pdb=" N LEU P 398 " pdb=" CA LEU P 398 " pdb=" C LEU P 398 " ideal model delta sigma weight residual 107.91 149.33 -41.42 2.05e+00 2.38e-01 4.08e+02 angle pdb=" N PRO P 399 " pdb=" CD PRO P 399 " pdb=" CG PRO P 399 " ideal model delta sigma weight residual 103.80 79.83 23.97 1.20e+00 6.94e-01 3.99e+02 angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" C PRO P 399 " ideal model delta sigma weight residual 112.10 162.47 -50.37 2.60e+00 1.48e-01 3.75e+02 ... (remaining 4281 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.87: 1509 10.87 - 21.73: 277 21.73 - 32.60: 73 32.60 - 43.46: 16 43.46 - 54.32: 6 Dihedral angle restraints: 1881 sinusoidal: 631 harmonic: 1250 Sorted by residual: dihedral pdb=" N VAL P 118 " pdb=" C VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta harmonic sigma weight residual 123.40 88.32 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" CA LYS P 394 " pdb=" C LYS P 394 " pdb=" N ASN P 395 " pdb=" CA ASN P 395 " ideal model delta harmonic sigma weight residual 180.00 -129.42 -50.58 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CA LEU P 398 " pdb=" CB LEU P 398 " ideal model delta harmonic sigma weight residual 122.80 144.26 -21.46 0 2.50e+00 1.60e-01 7.37e+01 ... (remaining 1878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 500 0.366 - 0.732: 1 0.732 - 1.098: 1 1.098 - 1.464: 0 1.464 - 1.829: 2 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO P 399 " pdb=" N PRO P 399 " pdb=" C PRO P 399 " pdb=" CB PRO P 399 " both_signs ideal model delta sigma weight residual False 2.72 0.89 1.83 2.00e-01 2.50e+01 8.37e+01 chirality pdb=" CA LEU P 398 " pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CB LEU P 398 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.79e+01 chirality pdb=" CA ASN P 133 " pdb=" N ASN P 133 " pdb=" C ASN P 133 " pdb=" CB ASN P 133 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 501 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 398 " 0.143 5.00e-02 4.00e+02 2.09e-01 7.02e+01 pdb=" N PRO P 399 " -0.359 5.00e-02 4.00e+02 pdb=" CA PRO P 399 " 0.147 5.00e-02 4.00e+02 pdb=" CD PRO P 399 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 261 " 0.029 2.00e-02 2.50e+03 2.01e-02 7.10e+00 pdb=" CG PHE P 261 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE P 261 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE P 261 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 261 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 261 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 256 " 0.023 2.00e-02 2.50e+03 1.86e-02 6.89e+00 pdb=" CG TYR P 256 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR P 256 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 256 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 256 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 256 " -0.001 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 45 2.46 - 3.07: 2532 3.07 - 3.68: 4232 3.68 - 4.29: 5645 4.29 - 4.90: 8788 Nonbonded interactions: 21242 Sorted by model distance: nonbonded pdb=" O ASN P 229 " pdb=" OD1 ASN P 229 " model vdw 1.855 3.040 nonbonded pdb=" CE2 TYR P 117 " pdb=" CG2 THR P 152 " model vdw 1.987 3.760 nonbonded pdb=" O LEU P 398 " pdb=" CD PRO P 399 " model vdw 2.081 2.752 nonbonded pdb=" O GLY P 233 " pdb=" NH1 ARG P 234 " model vdw 2.082 3.120 nonbonded pdb=" OG SER P 75 " pdb=" O VAL P 78 " model vdw 2.093 3.040 ... (remaining 21237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.150 Find NCS groups from input model: 0.010 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:1.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.015 0.200 3148 Z= 0.695 Angle : 2.407 50.367 4286 Z= 1.473 Chirality : 0.139 1.829 504 Planarity : 0.012 0.209 564 Dihedral : 12.691 54.322 1075 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 42.83 Ramachandran Plot: Outliers : 1.16 % Allowed : 16.94 % Favored : 81.90 % Rotamer: Outliers : 1.41 % Allowed : 6.01 % Favored : 92.58 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 1.93 % 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: -6.10 (0.25), residues: 431 helix: -4.70 (0.36), residues: 55 sheet: -1.38 (0.90), residues: 28 loop : -4.65 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG P 234 TYR 0.046 0.005 TYR P 256 PHE 0.044 0.006 PHE P 94 TRP 0.028 0.005 TRP P 440 HIS 0.011 0.005 HIS P 86 Details of bonding type rmsd/Z covalent geometry : bond 0.01454 / 0.69 ( 3148) covalent geometry : angle 2.40708 / 1.47 ( 4286) hydrogen bonds : bond 0.23777 / 13.16 ( 41) hydrogen bonds : angle 12.19687 / 7.40 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8674 (pm20) cc_final: 0.8415 (pm20) REVERT: P 65 TYR cc_start: 0.8667 (t80) cc_final: 0.8349 (t80) REVERT: P 109 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6511 (mtt90) REVERT: P 133 ASN cc_start: 0.7821 (m-40) cc_final: 0.7415 (m-40) REVERT: P 184 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7947 (mtpt) REVERT: P 268 THR cc_start: 0.8176 (p) cc_final: 0.7792 (p) REVERT: P 393 ASP cc_start: 0.7378 (m-30) cc_final: 0.7103 (m-30) REVERT: P 424 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8004 (ptmt) outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.0554 time to fit residues: 5.6683 Evaluate side-chains 59 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 399 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN P 229 ASN P 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.202762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188485 restraints weight = 4977.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.191437 restraints weight = 2946.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.193462 restraints weight = 1935.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194766 restraints weight = 1403.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195827 restraints weight = 1106.830| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.157 Angle : 0.901 10.215 4286 Z= 0.479 Chirality : 0.049 0.189 504 Planarity : 0.006 0.064 564 Dihedral : 9.353 33.850 464 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.76 % Favored : 86.77 % Rotamer: Outliers : 5.30 % Allowed : 12.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -5.27 (0.31), residues: 431 helix: -2.66 (0.62), residues: 54 sheet: -2.30 (0.75), residues: 50 loop : -4.24 (0.25), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 377 TYR 0.021 0.002 TYR P 441 PHE 0.020 0.002 PHE P 373 TRP 0.013 0.002 TRP P 452 HIS 0.003 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 3148) covalent geometry : angle 0.90068 / 0.48 ( 4286) hydrogen bonds : bond 0.03929 / 2.35 ( 41) hydrogen bonds : angle 6.18375 / 3.98 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.108 Fit side-chains REVERT: P 154 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: P 184 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7229 (mtpt) REVERT: P 219 MET cc_start: 0.6524 (tpp) cc_final: 0.6193 (mmt) REVERT: P 232 LEU cc_start: 0.6382 (tp) cc_final: 0.6177 (tp) REVERT: P 431 ASN cc_start: 0.7972 (m-40) cc_final: 0.7592 (m-40) outliers start: 15 outliers final: 5 residues processed: 81 average time/residue: 0.0494 time to fit residues: 4.8402 Evaluate side-chains 63 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.204747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.190332 restraints weight = 4870.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.193337 restraints weight = 2759.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.195147 restraints weight = 1782.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.196653 restraints weight = 1292.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.197502 restraints weight = 996.784| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3148 Z= 0.138 Angle : 0.803 12.388 4286 Z= 0.419 Chirality : 0.046 0.158 504 Planarity : 0.007 0.096 564 Dihedral : 7.992 28.134 459 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.99 % Favored : 86.31 % Rotamer: Outliers : 4.95 % Allowed : 17.31 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -5.02 (0.32), residues: 431 helix: -2.27 (0.66), residues: 61 sheet: -0.89 (1.21), residues: 23 loop : -4.14 (0.24), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 377 TYR 0.016 0.002 TYR P 83 PHE 0.012 0.002 PHE P 373 TRP 0.020 0.003 TRP P 57 HIS 0.003 0.001 HIS P 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3148) covalent geometry : angle 0.80296 / 0.42 ( 4286) hydrogen bonds : bond 0.03279 / 1.88 ( 41) hydrogen bonds : angle 5.56094 / 3.71 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.083 Fit side-chains REVERT: P 71 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7087 (ttm110) REVERT: P 154 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: P 219 MET cc_start: 0.6564 (tpp) cc_final: 0.6246 (mmt) REVERT: P 263 LYS cc_start: 0.7706 (pttm) cc_final: 0.7409 (ptmm) REVERT: P 431 ASN cc_start: 0.8300 (m-40) cc_final: 0.7885 (m-40) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.0667 time to fit residues: 6.0996 Evaluate side-chains 66 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 181 LEU Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 454 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.208529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.193883 restraints weight = 4812.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196867 restraints weight = 2736.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.198838 restraints weight = 1773.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.200036 restraints weight = 1282.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.200910 restraints weight = 1022.435| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3148 Z= 0.121 Angle : 0.762 13.235 4286 Z= 0.393 Chirality : 0.044 0.142 504 Planarity : 0.006 0.086 564 Dihedral : 7.110 28.255 459 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.06 % Favored : 87.24 % Rotamer: Outliers : 5.30 % Allowed : 19.79 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.66 (0.32), residues: 431 helix: -2.10 (0.61), residues: 61 sheet: -0.44 (1.10), residues: 28 loop : -3.91 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 377 TYR 0.011 0.001 TYR P 441 PHE 0.011 0.002 PHE P 373 TRP 0.022 0.003 TRP P 57 HIS 0.001 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 3148) covalent geometry : angle 0.76194 / 0.39 ( 4286) hydrogen bonds : bond 0.02926 / 1.73 ( 41) hydrogen bonds : angle 5.10507 / 3.47 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: P 71 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6630 (ttm110) REVERT: P 154 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.5912 (pm20) REVERT: P 173 LEU cc_start: 0.7249 (tt) cc_final: 0.6201 (tp) REVERT: P 263 LYS cc_start: 0.7561 (pttm) cc_final: 0.7246 (ptmm) REVERT: P 389 ILE cc_start: 0.7512 (mp) cc_final: 0.7086 (pt) REVERT: P 395 ASN cc_start: 0.4422 (t0) cc_final: 0.4094 (p0) REVERT: P 458 VAL cc_start: 0.6569 (OUTLIER) cc_final: 0.6231 (t) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.0581 time to fit residues: 5.1687 Evaluate side-chains 67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.205459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.190915 restraints weight = 4892.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.193921 restraints weight = 2801.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.195719 restraints weight = 1822.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.197172 restraints weight = 1325.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.198018 restraints weight = 1032.303| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.123 Angle : 0.721 13.643 4286 Z= 0.373 Chirality : 0.043 0.148 504 Planarity : 0.006 0.082 564 Dihedral : 6.833 25.871 459 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.15 % Favored : 85.15 % Rotamer: Outliers : 6.36 % Allowed : 20.85 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.46 (0.33), residues: 431 helix: -1.95 (0.60), residues: 61 sheet: -0.56 (1.08), residues: 28 loop : -3.74 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 377 TYR 0.015 0.002 TYR P 441 PHE 0.012 0.002 PHE P 261 TRP 0.025 0.003 TRP P 57 HIS 0.002 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 3148) covalent geometry : angle 0.72126 / 0.37 ( 4286) hydrogen bonds : bond 0.02964 / 1.70 ( 41) hydrogen bonds : angle 4.80382 / 3.22 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.120 Fit side-chains REVERT: P 71 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6639 (ttm110) REVERT: P 154 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: P 263 LYS cc_start: 0.7523 (pttm) cc_final: 0.7258 (ptmm) REVERT: P 265 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.5799 (t-90) REVERT: P 395 ASN cc_start: 0.4419 (t0) cc_final: 0.4097 (p0) REVERT: P 403 ASP cc_start: 0.7360 (p0) cc_final: 0.7134 (p0) REVERT: P 458 VAL cc_start: 0.6622 (OUTLIER) cc_final: 0.6336 (t) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 0.0564 time to fit residues: 5.1667 Evaluate side-chains 67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 26 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.8682 > 50:) chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.205879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.191117 restraints weight = 4932.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.194111 restraints weight = 2827.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195916 restraints weight = 1843.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197429 restraints weight = 1346.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.198310 restraints weight = 1045.310| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3148 Z= 0.127 Angle : 0.727 13.533 4286 Z= 0.372 Chirality : 0.044 0.146 504 Planarity : 0.006 0.105 564 Dihedral : 6.703 25.565 459 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.15 % Favored : 85.15 % Rotamer: Outliers : 6.01 % Allowed : 21.55 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.38 (0.33), residues: 431 helix: -1.87 (0.60), residues: 61 sheet: -0.39 (1.10), residues: 28 loop : -3.71 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 377 TYR 0.014 0.002 TYR P 441 PHE 0.018 0.002 PHE P 373 TRP 0.024 0.003 TRP P 57 HIS 0.001 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 3148) covalent geometry : angle 0.72725 / 0.37 ( 4286) hydrogen bonds : bond 0.02815 / 1.62 ( 41) hydrogen bonds : angle 4.74978 / 3.17 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.067 Fit side-chains REVERT: P 71 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6796 (ttm110) REVERT: P 115 MET cc_start: 0.7767 (mmt) cc_final: 0.7284 (mmt) REVERT: P 154 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: P 265 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.5969 (t-90) REVERT: P 371 MET cc_start: 0.5601 (mtt) cc_final: 0.5054 (mmm) REVERT: P 395 ASN cc_start: 0.5087 (t0) cc_final: 0.4220 (p0) REVERT: P 396 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6142 (tm-30) REVERT: P 458 VAL cc_start: 0.6675 (OUTLIER) cc_final: 0.6353 (t) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 0.0560 time to fit residues: 4.7994 Evaluate side-chains 65 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.185756 restraints weight = 4941.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.188585 restraints weight = 2864.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.190346 restraints weight = 1891.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.191762 restraints weight = 1398.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.192669 restraints weight = 1097.743| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3148 Z= 0.168 Angle : 0.787 12.984 4286 Z= 0.408 Chirality : 0.046 0.157 504 Planarity : 0.007 0.109 564 Dihedral : 7.039 24.468 459 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.24 % Favored : 83.06 % Rotamer: Outliers : 8.13 % Allowed : 21.91 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.41 (0.34), residues: 431 helix: -1.85 (0.61), residues: 59 sheet: -0.37 (1.10), residues: 28 loop : -3.73 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 259 TYR 0.021 0.002 TYR P 256 PHE 0.018 0.003 PHE P 227 TRP 0.026 0.004 TRP P 57 HIS 0.003 0.001 HIS P 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 3148) covalent geometry : angle 0.78733 / 0.41 ( 4286) hydrogen bonds : bond 0.03139 / 1.75 ( 41) hydrogen bonds : angle 4.97350 / 3.31 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.109 Fit side-chains REVERT: P 71 ARG cc_start: 0.7375 (mtm110) cc_final: 0.6921 (ttm110) REVERT: P 109 ARG cc_start: 0.5991 (mtt180) cc_final: 0.5736 (mtt180) REVERT: P 154 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: P 198 LYS cc_start: 0.8374 (ttpp) cc_final: 0.6910 (tppt) REVERT: P 265 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6327 (t-90) REVERT: P 268 THR cc_start: 0.8070 (p) cc_final: 0.7666 (p) REVERT: P 395 ASN cc_start: 0.5153 (t0) cc_final: 0.3819 (p0) REVERT: P 431 ASN cc_start: 0.7929 (m110) cc_final: 0.7698 (m-40) REVERT: P 458 VAL cc_start: 0.6885 (OUTLIER) cc_final: 0.6549 (t) outliers start: 23 outliers final: 14 residues processed: 74 average time/residue: 0.0522 time to fit residues: 4.8069 Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.0060 chunk 1 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.205067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.190266 restraints weight = 5121.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.193265 restraints weight = 2951.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.195210 restraints weight = 1935.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.196743 restraints weight = 1412.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.197643 restraints weight = 1091.156| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3148 Z= 0.113 Angle : 0.741 13.626 4286 Z= 0.366 Chirality : 0.043 0.123 504 Planarity : 0.006 0.097 564 Dihedral : 6.364 25.316 459 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.53 % Favored : 86.77 % Rotamer: Outliers : 5.65 % Allowed : 22.97 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.20 (0.34), residues: 431 helix: -1.57 (0.63), residues: 61 sheet: -0.11 (1.16), residues: 28 loop : -3.63 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 377 TYR 0.011 0.001 TYR P 441 PHE 0.012 0.001 PHE P 373 TRP 0.029 0.003 TRP P 57 HIS 0.001 0.000 HIS P 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 3148) covalent geometry : angle 0.74146 / 0.37 ( 4286) hydrogen bonds : bond 0.02692 / 1.57 ( 41) hydrogen bonds : angle 4.75210 / 3.13 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.105 Fit side-chains REVERT: P 71 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6754 (ttm110) REVERT: P 82 GLN cc_start: 0.7660 (mt0) cc_final: 0.7254 (pp30) REVERT: P 117 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: P 154 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: P 395 ASN cc_start: 0.4622 (t0) cc_final: 0.4118 (p0) REVERT: P 422 MET cc_start: 0.7510 (mmm) cc_final: 0.7237 (mmm) REVERT: P 454 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7036 (ptm-80) REVERT: P 458 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6484 (t) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.0602 time to fit residues: 5.1997 Evaluate side-chains 64 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.205992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.191101 restraints weight = 5065.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194119 restraints weight = 2896.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.196202 restraints weight = 1877.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197295 restraints weight = 1342.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.198309 restraints weight = 1074.632| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3148 Z= 0.133 Angle : 0.763 13.936 4286 Z= 0.378 Chirality : 0.044 0.138 504 Planarity : 0.006 0.107 564 Dihedral : 6.407 23.059 459 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.62 % Favored : 84.69 % Rotamer: Outliers : 5.65 % Allowed : 23.67 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.19 (0.34), residues: 431 helix: -1.54 (0.63), residues: 59 sheet: -0.21 (1.14), residues: 28 loop : -3.60 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 377 TYR 0.013 0.002 TYR P 441 PHE 0.014 0.002 PHE P 261 TRP 0.029 0.003 TRP P 57 HIS 0.003 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3148) covalent geometry : angle 0.76290 / 0.38 ( 4286) hydrogen bonds : bond 0.02779 / 1.59 ( 41) hydrogen bonds : angle 4.76636 / 3.14 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.113 Fit side-chains REVERT: P 30 TYR cc_start: 0.4063 (OUTLIER) cc_final: 0.3765 (m-80) REVERT: P 71 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6922 (ttm110) REVERT: P 82 GLN cc_start: 0.7736 (mt0) cc_final: 0.7147 (pp30) REVERT: P 117 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.5936 (m-10) REVERT: P 154 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: P 198 LYS cc_start: 0.8370 (ttpp) cc_final: 0.7016 (tppt) REVERT: P 268 THR cc_start: 0.8027 (p) cc_final: 0.7671 (p) REVERT: P 395 ASN cc_start: 0.4577 (t0) cc_final: 0.3991 (p0) REVERT: P 396 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6140 (tm-30) REVERT: P 454 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7015 (ptm-80) REVERT: P 458 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6616 (t) outliers start: 16 outliers final: 8 residues processed: 66 average time/residue: 0.0454 time to fit residues: 3.7683 Evaluate side-chains 67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.189605 restraints weight = 5041.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.192361 restraints weight = 2992.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.194223 restraints weight = 1991.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.195317 restraints weight = 1465.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.196192 restraints weight = 1184.583| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3148 Z= 0.151 Angle : 0.787 13.493 4286 Z= 0.394 Chirality : 0.045 0.149 504 Planarity : 0.007 0.108 564 Dihedral : 6.693 22.417 459 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.01 % Favored : 83.29 % Rotamer: Outliers : 5.65 % Allowed : 24.03 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.22 (0.35), residues: 431 helix: -1.59 (0.64), residues: 59 sheet: -0.25 (1.12), residues: 28 loop : -3.62 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 259 TYR 0.015 0.002 TYR P 256 PHE 0.016 0.002 PHE P 261 TRP 0.031 0.003 TRP P 57 HIS 0.003 0.001 HIS P 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3148) covalent geometry : angle 0.78686 / 0.39 ( 4286) hydrogen bonds : bond 0.02877 / 1.62 ( 41) hydrogen bonds : angle 4.90919 / 3.22 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.115 Fit side-chains REVERT: P 30 TYR cc_start: 0.3882 (OUTLIER) cc_final: 0.3168 (m-80) REVERT: P 71 ARG cc_start: 0.7246 (mtm110) cc_final: 0.6875 (ttm110) REVERT: P 116 LYS cc_start: 0.5899 (mttt) cc_final: 0.5655 (mttt) REVERT: P 117 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6251 (m-10) REVERT: P 154 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6437 (pm20) REVERT: P 219 MET cc_start: 0.5456 (tpt) cc_final: 0.5168 (tpt) REVERT: P 268 THR cc_start: 0.8140 (p) cc_final: 0.7785 (p) REVERT: P 395 ASN cc_start: 0.4570 (t0) cc_final: 0.3962 (p0) REVERT: P 396 GLU cc_start: 0.6331 (tm-30) cc_final: 0.6104 (tm-30) REVERT: P 454 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7058 (ptm-80) REVERT: P 458 VAL cc_start: 0.6963 (OUTLIER) cc_final: 0.6660 (t) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.0487 time to fit residues: 4.0330 Evaluate side-chains 66 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0070 chunk 22 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.210024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194880 restraints weight = 5129.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.198072 restraints weight = 2930.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200227 restraints weight = 1894.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.201427 restraints weight = 1349.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202358 restraints weight = 1070.298| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.125 Angle : 0.750 13.925 4286 Z= 0.373 Chirality : 0.044 0.133 504 Planarity : 0.006 0.103 564 Dihedral : 6.373 24.716 459 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.69 % Favored : 85.61 % Rotamer: Outliers : 5.65 % Allowed : 24.73 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.12 (0.34), residues: 431 helix: -1.54 (0.63), residues: 61 sheet: 0.55 (1.47), residues: 18 loop : -3.50 (0.27), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 377 TYR 0.013 0.002 TYR P 218 PHE 0.012 0.002 PHE P 373 TRP 0.030 0.003 TRP P 57 HIS 0.001 0.000 HIS P 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 3148) covalent geometry : angle 0.75013 / 0.37 ( 4286) hydrogen bonds : bond 0.02679 / 1.57 ( 41) hydrogen bonds : angle 4.76994 / 3.14 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 674.82 seconds wall clock time: 12 minutes 11.11 seconds (731.11 seconds total)