Starting phenix.real_space_refine on Mon Feb 10 22:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_4053.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_4053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_4053.map" model { file = "/net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_4053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lii_4053/02_2025/5lii_4053.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.270 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 2.27, per 1000 atoms: 0.73 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: 0.73 Conformation dependent library (CDL) restraints added in 385.8 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: 0.32 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: 0.65 Time building geometry restraints manager: 0.86 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: 0.080 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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= 0.963 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.005 TRP P 440 HIS 0.011 0.005 HIS P 86 PHE 0.044 0.006 PHE P 94 TYR 0.046 0.005 TYR P 256 ARG 0.010 0.002 ARG P 234 *********************** 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 : 0.383 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: 0.1496 time to fit residues: 15.2898 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 : 0.364 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 194 GLN P 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.201455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.187028 restraints weight = 4958.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.190272 restraints weight = 2814.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.192350 restraints weight = 1808.208| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3148 Z= 0.236 Angle : 0.932 10.519 4286 Z= 0.497 Chirality : 0.049 0.205 504 Planarity : 0.006 0.069 564 Dihedral : 9.612 34.039 464 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.62 % Favored : 84.92 % Rotamer: Outliers : 5.65 % Allowed : 12.01 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.31), residues: 431 helix: -2.75 (0.61), residues: 54 sheet: -2.38 (0.75), residues: 50 loop : -4.32 (0.25), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 452 HIS 0.003 0.001 HIS P 265 PHE 0.019 0.003 PHE P 373 TYR 0.024 0.003 TYR P 441 ARG 0.004 0.001 ARG P 377 *********************** 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 85 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: P 154 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6477 (pm20) REVERT: P 184 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7302 (mtpt) REVERT: P 219 MET cc_start: 0.6539 (tpp) cc_final: 0.6283 (mmt) REVERT: P 232 LEU cc_start: 0.6520 (tp) cc_final: 0.6295 (tp) REVERT: P 384 GLN cc_start: 0.5213 (OUTLIER) cc_final: 0.4260 (pp30) REVERT: P 431 ASN cc_start: 0.8108 (m-40) cc_final: 0.7789 (m-40) outliers start: 16 outliers final: 6 residues processed: 82 average time/residue: 0.1792 time to fit residues: 17.5224 Evaluate side-chains 61 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 SER 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 373 PHE Chi-restraints excluded: chain P residue 384 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.0040 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.198756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183981 restraints weight = 4753.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.187071 restraints weight = 2709.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.189093 restraints weight = 1741.772| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3148 Z= 0.178 Angle : 0.804 10.482 4286 Z= 0.424 Chirality : 0.045 0.157 504 Planarity : 0.007 0.098 564 Dihedral : 8.143 29.148 459 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.30 % Favored : 87.01 % Rotamer: Outliers : 4.95 % Allowed : 16.25 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.31), residues: 431 helix: -2.34 (0.64), residues: 61 sheet: -0.78 (1.22), residues: 23 loop : -4.17 (0.24), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP P 57 HIS 0.004 0.001 HIS P 415 PHE 0.013 0.002 PHE P 373 TYR 0.016 0.002 TYR P 83 ARG 0.005 0.000 ARG P 377 *********************** 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 78 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.316 Fit side-chains REVERT: P 37 GLN cc_start: 0.8436 (pm20) cc_final: 0.8233 (pm20) REVERT: P 71 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7154 (ttm110) REVERT: P 154 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: P 219 MET cc_start: 0.6478 (tpp) cc_final: 0.6186 (mmt) outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 0.1566 time to fit residues: 14.2748 Evaluate side-chains 65 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 384 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 35 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2610 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.204728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.190390 restraints weight = 4837.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.193335 restraints weight = 2737.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195437 restraints weight = 1762.042| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3148 Z= 0.171 Angle : 0.758 13.057 4286 Z= 0.390 Chirality : 0.044 0.143 504 Planarity : 0.006 0.085 564 Dihedral : 7.196 28.241 459 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.70 % Allowed : 11.83 % Favored : 87.47 % Rotamer: Outliers : 5.65 % Allowed : 19.08 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.32), residues: 431 helix: -2.14 (0.61), residues: 61 sheet: -0.65 (1.26), residues: 23 loop : -3.91 (0.25), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 57 HIS 0.001 0.000 HIS P 415 PHE 0.012 0.001 PHE P 373 TYR 0.012 0.001 TYR P 441 ARG 0.005 0.000 ARG P 377 *********************** 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 80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.349 Fit side-chains REVERT: P 71 ARG cc_start: 0.7367 (mtm110) cc_final: 0.6803 (ttm110) REVERT: P 154 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: P 219 MET cc_start: 0.6457 (tpp) cc_final: 0.6116 (mmt) REVERT: P 395 ASN cc_start: 0.4713 (t0) cc_final: 0.4373 (p0) REVERT: P 458 VAL cc_start: 0.6615 (OUTLIER) cc_final: 0.6288 (t) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.1573 time to fit residues: 14.1703 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 : 0.319 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.207454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192748 restraints weight = 4862.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195837 restraints weight = 2766.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.197785 restraints weight = 1788.497| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.5154 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= 0.181 Angle : 0.758 13.223 4286 Z= 0.391 Chirality : 0.044 0.149 504 Planarity : 0.006 0.084 564 Dihedral : 6.983 25.868 459 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.69 % Favored : 85.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.33), residues: 431 helix: -2.09 (0.61), residues: 61 sheet: -0.29 (1.13), residues: 28 loop : -3.76 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 57 HIS 0.002 0.001 HIS P 224 PHE 0.014 0.002 PHE P 227 TYR 0.017 0.002 TYR P 441 ARG 0.005 0.000 ARG P 377 *********************** 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 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: P 71 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6660 (ttm110) REVERT: P 154 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: P 265 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.5509 (t-90) REVERT: P 395 ASN cc_start: 0.4523 (t0) cc_final: 0.4064 (p0) REVERT: P 396 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6288 (tm-30) REVERT: P 458 VAL cc_start: 0.6557 (OUTLIER) cc_final: 0.6250 (t) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.1436 time to fit residues: 13.3511 Evaluate side-chains 69 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 265 HIS Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER 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 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.206415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.192224 restraints weight = 5033.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.195079 restraints weight = 2876.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196998 restraints weight = 1884.133| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.5331 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= 0.181 Angle : 0.753 13.052 4286 Z= 0.384 Chirality : 0.044 0.144 504 Planarity : 0.007 0.105 564 Dihedral : 6.806 25.495 459 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.69 % Favored : 85.61 % Rotamer: Outliers : 6.71 % Allowed : 21.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.33), residues: 431 helix: -1.97 (0.61), residues: 61 sheet: -0.48 (1.08), residues: 28 loop : -3.71 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 57 HIS 0.001 0.001 HIS P 91 PHE 0.017 0.002 PHE P 373 TYR 0.014 0.002 TYR P 441 ARG 0.003 0.000 ARG P 377 *********************** 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 80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: P 71 ARG cc_start: 0.7279 (mtm110) cc_final: 0.6799 (ttm110) REVERT: P 154 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6529 (pm20) REVERT: P 265 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6138 (t-90) REVERT: P 371 MET cc_start: 0.5677 (mtt) cc_final: 0.5131 (mmm) REVERT: P 395 ASN cc_start: 0.5233 (t0) cc_final: 0.4316 (p0) REVERT: P 458 VAL cc_start: 0.6724 (OUTLIER) cc_final: 0.6396 (t) outliers start: 19 outliers final: 12 residues processed: 74 average time/residue: 0.1308 time to fit residues: 12.0910 Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 265 HIS Chi-restraints excluded: chain P residue 433 SER 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 14 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.201052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.185957 restraints weight = 4969.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188894 restraints weight = 2829.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.190914 restraints weight = 1838.025| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.5335 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= 0.209 Angle : 0.766 13.066 4286 Z= 0.393 Chirality : 0.045 0.154 504 Planarity : 0.007 0.108 564 Dihedral : 6.874 24.832 459 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.39 % Favored : 84.92 % Rotamer: Outliers : 7.42 % Allowed : 22.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.34), residues: 431 helix: -1.96 (0.62), residues: 61 sheet: -0.36 (1.08), residues: 28 loop : -3.70 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.014 0.002 PHE P 373 TYR 0.017 0.002 TYR P 441 ARG 0.003 0.000 ARG P 377 *********************** 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 83 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: P 71 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6945 (ttm110) REVERT: P 82 GLN cc_start: 0.7678 (mt0) cc_final: 0.6859 (pp30) REVERT: P 109 ARG cc_start: 0.5821 (mpt180) cc_final: 0.5128 (mtt90) REVERT: P 154 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: P 173 LEU cc_start: 0.7413 (tp) cc_final: 0.7119 (tt) REVERT: P 265 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.6144 (t-90) REVERT: P 395 ASN cc_start: 0.4719 (t0) cc_final: 0.3826 (p0) REVERT: P 396 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6047 (tm-30) REVERT: P 458 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.6431 (t) outliers start: 21 outliers final: 14 residues processed: 75 average time/residue: 0.1379 time to fit residues: 12.7820 Evaluate side-chains 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 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 126 ILE 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 433 SER 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 22 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5630 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.209411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.194317 restraints weight = 5132.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.197441 restraints weight = 2880.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199538 restraints weight = 1848.333| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.5762 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= 0.168 Angle : 0.754 14.427 4286 Z= 0.375 Chirality : 0.043 0.137 504 Planarity : 0.006 0.107 564 Dihedral : 6.459 24.496 459 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.99 % Favored : 86.31 % Rotamer: Outliers : 6.71 % Allowed : 23.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.34), residues: 431 helix: -1.76 (0.62), residues: 61 sheet: -0.17 (1.13), residues: 28 loop : -3.62 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.001 0.001 HIS P 265 PHE 0.010 0.001 PHE P 227 TYR 0.013 0.002 TYR P 218 ARG 0.003 0.000 ARG P 377 *********************** 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 78 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.367 Fit side-chains REVERT: P 30 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.3700 (m-80) REVERT: P 71 ARG cc_start: 0.7297 (mtm110) cc_final: 0.6782 (ttm110) REVERT: P 82 GLN cc_start: 0.7694 (mt0) cc_final: 0.7203 (pp30) REVERT: P 109 ARG cc_start: 0.5790 (mpt180) cc_final: 0.5117 (mtt90) REVERT: P 154 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: P 173 LEU cc_start: 0.7280 (tp) cc_final: 0.7026 (tt) REVERT: P 265 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.6342 (t-90) REVERT: P 395 ASN cc_start: 0.4699 (t0) cc_final: 0.3970 (p0) REVERT: P 396 GLU cc_start: 0.6079 (tm-30) cc_final: 0.5822 (tm-30) REVERT: P 454 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7046 (ptm-80) REVERT: P 458 VAL cc_start: 0.6707 (OUTLIER) cc_final: 0.6382 (t) outliers start: 19 outliers final: 10 residues processed: 73 average time/residue: 0.1384 time to fit residues: 12.9612 Evaluate side-chains 70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 34 optimal weight: 0.0070 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.1974 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.220280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.205332 restraints weight = 4923.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208364 restraints weight = 2807.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.210463 restraints weight = 1833.452| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3148 Z= 0.147 Angle : 0.736 15.037 4286 Z= 0.359 Chirality : 0.043 0.129 504 Planarity : 0.006 0.100 564 Dihedral : 5.861 23.080 459 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.46 % Favored : 85.85 % Rotamer: Outliers : 4.59 % Allowed : 26.15 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.34), residues: 431 helix: -1.65 (0.63), residues: 64 sheet: 0.62 (1.48), residues: 18 loop : -3.46 (0.27), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP P 57 HIS 0.001 0.000 HIS P 265 PHE 0.011 0.001 PHE P 373 TYR 0.009 0.001 TYR P 441 ARG 0.004 0.000 ARG P 377 *********************** 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 69 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.312 Fit side-chains REVERT: P 71 ARG cc_start: 0.7001 (mtm110) cc_final: 0.6742 (ttm110) REVERT: P 82 GLN cc_start: 0.7615 (mt0) cc_final: 0.7254 (pp30) REVERT: P 154 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: P 265 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5981 (t-170) REVERT: P 395 ASN cc_start: 0.4254 (t0) cc_final: 0.3796 (p0) REVERT: P 454 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6812 (ptm-80) REVERT: P 458 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6541 (t) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.1327 time to fit residues: 11.0544 Evaluate side-chains 65 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 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 = 0.4254 r_free = 0.4254 target = 0.209597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.194431 restraints weight = 5107.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.197425 restraints weight = 2919.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.199488 restraints weight = 1907.479| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.199 Angle : 0.777 15.558 4286 Z= 0.385 Chirality : 0.044 0.144 504 Planarity : 0.006 0.104 564 Dihedral : 6.139 23.102 459 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.39 % Favored : 84.92 % Rotamer: Outliers : 4.24 % Allowed : 26.86 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.34), residues: 431 helix: -1.98 (0.58), residues: 67 sheet: 0.45 (1.42), residues: 18 loop : -3.34 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.003 0.001 HIS P 224 PHE 0.014 0.002 PHE P 261 TYR 0.015 0.002 TYR P 218 ARG 0.003 0.000 ARG P 377 ********************** 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 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.343 Fit side-chains REVERT: P 71 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6823 (ttm110) REVERT: P 82 GLN cc_start: 0.7964 (mt0) cc_final: 0.7347 (pp30) REVERT: P 154 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: P 194 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7397 (mm110) REVERT: P 265 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6114 (t-90) REVERT: P 454 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6703 (ptm-80) REVERT: P 458 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6566 (t) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.1428 time to fit residues: 12.2949 Evaluate side-chains 65 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 THR 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 188 ILE Chi-restraints excluded: chain P residue 265 HIS 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 30 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.203235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.188416 restraints weight = 5087.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.191093 restraints weight = 2936.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192760 restraints weight = 1963.452| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.6227 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= 0.176 Angle : 0.722 13.472 4286 Z= 0.364 Chirality : 0.043 0.141 504 Planarity : 0.006 0.102 564 Dihedral : 5.997 23.499 459 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.92 % Favored : 85.38 % Rotamer: Outliers : 5.30 % Allowed : 26.15 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.35), residues: 431 helix: -1.61 (0.64), residues: 61 sheet: 0.56 (1.45), residues: 18 loop : -3.22 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.002 0.001 HIS P 265 PHE 0.013 0.002 PHE P 373 TYR 0.015 0.002 TYR P 218 ARG 0.003 0.000 ARG P 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.86 seconds wall clock time: 24 minutes 55.15 seconds (1495.15 seconds total)