Starting phenix.real_space_refine on Mon Sep 23 13:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_4053.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_4053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_4053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_4053.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/09_2024/5lii_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-5461/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: 2.62, per 1000 atoms: 0.85 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: 0.83 Conformation dependent library (CDL) restraints added in 409.1 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: 0.30 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: 0.61 Time building geometry restraints manager: 0.98 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: 0.120 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.375 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: 0.1487 time to fit residues: 15.1739 Evaluate side-chains 59 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 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 fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: P 154 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: P 184 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7299 (mtpt) REVERT: P 219 MET cc_start: 0.6554 (tpp) cc_final: 0.6215 (mmt) REVERT: P 232 LEU cc_start: 0.6700 (tp) cc_final: 0.6383 (tp) REVERT: P 384 GLN cc_start: 0.5100 (OUTLIER) cc_final: 0.4227 (pp30) REVERT: P 431 ASN cc_start: 0.8135 (m-40) cc_final: 0.7802 (m-40) outliers start: 16 outliers final: 6 residues processed: 82 average time/residue: 0.1810 time to fit residues: 17.4047 Evaluate side-chains 61 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3894 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= 0.212 Angle : 0.840 10.635 4286 Z= 0.444 Chirality : 0.047 0.166 504 Planarity : 0.007 0.102 564 Dihedral : 8.397 28.859 459 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.92 % Favored : 85.38 % Rotamer: Outliers : 5.65 % Allowed : 16.96 % Favored : 77.39 % 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: -5.14 (0.32), residues: 431 helix: -2.41 (0.64), residues: 61 sheet: -0.73 (1.08), residues: 28 loop : -4.28 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP P 57 HIS 0.005 0.001 HIS P 415 PHE 0.014 0.002 PHE P 373 TYR 0.018 0.002 TYR P 83 ARG 0.007 0.001 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 81 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8480 (pm20) cc_final: 0.8193 (pm20) REVERT: P 71 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7568 (ttm110) REVERT: P 93 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7389 (tpp80) REVERT: P 109 ARG cc_start: 0.6681 (mtp180) cc_final: 0.6430 (mpt180) REVERT: P 154 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: P 173 LEU cc_start: 0.7416 (tp) cc_final: 0.7178 (tt) REVERT: P 219 MET cc_start: 0.6528 (tpp) cc_final: 0.6159 (mmt) REVERT: P 431 ASN cc_start: 0.8274 (m-40) cc_final: 0.7841 (m-40) outliers start: 16 outliers final: 9 residues processed: 77 average time/residue: 0.1632 time to fit residues: 14.9190 Evaluate side-chains 69 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 384 GLN 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 38 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4440 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= 0.186 Angle : 0.796 13.031 4286 Z= 0.414 Chirality : 0.045 0.149 504 Planarity : 0.006 0.087 564 Dihedral : 7.658 28.297 459 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.30 % Favored : 87.01 % Rotamer: Outliers : 7.42 % Allowed : 18.73 % Favored : 73.85 % 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: -4.78 (0.33), residues: 431 helix: -1.89 (0.69), residues: 54 sheet: -0.45 (1.15), residues: 28 loop : -4.04 (0.25), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP P 57 HIS 0.001 0.000 HIS P 91 PHE 0.012 0.002 PHE P 373 TYR 0.018 0.002 TYR P 441 ARG 0.004 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 87 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.350 Fit side-chains REVERT: P 71 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7280 (ttm110) REVERT: P 109 ARG cc_start: 0.6747 (mtp180) cc_final: 0.6341 (mpt180) REVERT: P 154 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: P 173 LEU cc_start: 0.7347 (tp) cc_final: 0.7076 (tt) REVERT: P 219 MET cc_start: 0.6413 (tpp) cc_final: 0.6014 (mmt) REVERT: P 395 ASN cc_start: 0.4818 (t0) cc_final: 0.4128 (p0) REVERT: P 396 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6762 (tm-30) REVERT: P 458 VAL cc_start: 0.6430 (OUTLIER) cc_final: 0.6141 (t) REVERT: P 459 ARG cc_start: 0.6904 (mtp-110) cc_final: 0.6558 (ttp-170) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.1635 time to fit residues: 15.8208 Evaluate side-chains 73 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain P residue 188 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3148 Z= 0.208 Angle : 0.791 13.316 4286 Z= 0.414 Chirality : 0.046 0.157 504 Planarity : 0.006 0.087 564 Dihedral : 7.418 26.652 459 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.08 % Favored : 84.22 % Rotamer: Outliers : 6.71 % Allowed : 20.49 % 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: -4.69 (0.33), residues: 431 helix: -2.19 (0.62), residues: 61 sheet: -0.29 (1.16), residues: 28 loop : -3.94 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 57 HIS 0.002 0.001 HIS P 415 PHE 0.015 0.002 PHE P 261 TYR 0.021 0.002 TYR P 441 ARG 0.004 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 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: P 154 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: P 265 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6166 (t-90) REVERT: P 395 ASN cc_start: 0.4556 (t0) cc_final: 0.3665 (p0) REVERT: P 396 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6795 (mm-30) REVERT: P 458 VAL cc_start: 0.6437 (OUTLIER) cc_final: 0.6143 (t) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.1315 time to fit residues: 12.1560 Evaluate side-chains 72 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 373 PHE Chi-restraints excluded: chain P residue 384 GLN 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 24 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.003 0.038 3148 Z= 0.201 Angle : 0.757 12.997 4286 Z= 0.397 Chirality : 0.045 0.151 504 Planarity : 0.006 0.084 564 Dihedral : 7.240 26.193 459 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.15 % Favored : 85.15 % Rotamer: Outliers : 7.07 % Allowed : 21.55 % 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: -4.58 (0.34), residues: 431 helix: -2.08 (0.61), residues: 61 sheet: -0.40 (1.13), residues: 28 loop : -3.84 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.014 0.002 PHE P 261 TYR 0.016 0.002 TYR P 441 ARG 0.004 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 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.356 Fit side-chains REVERT: P 71 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7164 (ttm110) REVERT: P 110 GLN cc_start: 0.6733 (pt0) cc_final: 0.6505 (pt0) REVERT: P 154 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: P 265 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6080 (t-90) REVERT: P 371 MET cc_start: 0.5833 (mtt) cc_final: 0.5434 (mmm) REVERT: P 395 ASN cc_start: 0.4393 (t0) cc_final: 0.4126 (p0) REVERT: P 396 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6417 (tm-30) outliers start: 20 outliers final: 14 residues processed: 74 average time/residue: 0.1264 time to fit residues: 11.7842 Evaluate side-chains 71 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3148 Z= 0.268 Angle : 0.826 12.694 4286 Z= 0.433 Chirality : 0.047 0.164 504 Planarity : 0.007 0.089 564 Dihedral : 7.571 25.647 459 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.94 % Favored : 82.37 % Rotamer: Outliers : 8.13 % Allowed : 22.26 % 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: -4.60 (0.34), residues: 431 helix: -2.30 (0.61), residues: 61 sheet: -0.29 (1.15), residues: 28 loop : -3.83 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP P 57 HIS 0.004 0.001 HIS P 224 PHE 0.020 0.003 PHE P 261 TYR 0.020 0.003 TYR P 441 ARG 0.002 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 fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.400 Fit side-chains REVERT: P 71 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7200 (ttm110) REVERT: P 110 GLN cc_start: 0.6681 (pt0) cc_final: 0.6457 (pt0) REVERT: P 154 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: P 198 LYS cc_start: 0.8419 (ttpp) cc_final: 0.6665 (tppt) REVERT: P 265 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6497 (t-90) REVERT: P 371 MET cc_start: 0.5844 (mtt) cc_final: 0.5460 (mmm) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 0.1263 time to fit residues: 11.9866 Evaluate side-chains 72 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 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 205 VAL 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 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.5448 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= 0.176 Angle : 0.761 13.115 4286 Z= 0.390 Chirality : 0.044 0.138 504 Planarity : 0.006 0.081 564 Dihedral : 6.877 26.810 459 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.30 % Favored : 87.01 % 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: -4.47 (0.34), residues: 431 helix: -2.02 (0.62), residues: 61 sheet: -0.21 (1.15), residues: 28 loop : -3.78 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.001 HIS P 224 PHE 0.014 0.002 PHE P 373 TYR 0.012 0.002 TYR P 83 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 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.345 Fit side-chains REVERT: P 30 TYR cc_start: 0.3760 (OUTLIER) cc_final: 0.3291 (m-10) REVERT: P 71 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7093 (ttm110) REVERT: P 110 GLN cc_start: 0.6591 (pt0) cc_final: 0.6326 (pt0) REVERT: P 154 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: P 198 LYS cc_start: 0.8303 (ttpp) cc_final: 0.6505 (tppt) REVERT: P 263 LYS cc_start: 0.7653 (ptpp) cc_final: 0.7439 (ptpp) REVERT: P 265 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6444 (t-90) REVERT: P 431 ASN cc_start: 0.7863 (m110) cc_final: 0.7296 (t0) REVERT: P 454 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7082 (ptm-80) REVERT: P 457 ASN cc_start: 0.6647 (m110) cc_final: 0.5510 (m110) outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 0.1294 time to fit residues: 11.7140 Evaluate side-chains 76 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 148 VAL Chi-restraints excluded: chain P residue 153 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 205 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.5688 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= 0.183 Angle : 0.749 13.579 4286 Z= 0.384 Chirality : 0.044 0.141 504 Planarity : 0.006 0.082 564 Dihedral : 6.632 24.973 459 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.39 % Favored : 84.92 % Rotamer: Outliers : 7.07 % Allowed : 22.61 % 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: -1.87 (0.62), residues: 61 sheet: -0.24 (1.13), residues: 28 loop : -3.73 (0.26), residues: 342 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 0.015 0.002 PHE P 227 TYR 0.012 0.002 TYR P 441 ARG 0.003 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 79 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.358 Fit side-chains REVERT: P 71 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7082 (ttm110) REVERT: P 110 GLN cc_start: 0.6586 (pt0) cc_final: 0.6329 (pt0) REVERT: P 154 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: P 198 LYS cc_start: 0.8414 (ttpp) cc_final: 0.6775 (tppt) REVERT: P 396 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6032 (tm-30) REVERT: P 431 ASN cc_start: 0.7974 (m110) cc_final: 0.7223 (t0) REVERT: P 454 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6997 (ptm-80) REVERT: P 457 ASN cc_start: 0.6532 (m110) cc_final: 0.5452 (m110) outliers start: 20 outliers final: 12 residues processed: 74 average time/residue: 0.1262 time to fit residues: 11.7287 Evaluate side-chains 71 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 205 VAL Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5798 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= 0.187 Angle : 0.746 13.579 4286 Z= 0.384 Chirality : 0.044 0.144 504 Planarity : 0.006 0.083 564 Dihedral : 6.521 24.072 459 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.23 % Favored : 86.08 % 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 (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: -4.11 (0.35), residues: 431 helix: -1.23 (0.71), residues: 52 sheet: -0.24 (1.15), residues: 28 loop : -3.55 (0.27), residues: 351 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 0.014 0.002 PHE P 227 TYR 0.013 0.002 TYR P 441 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 72 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.362 Fit side-chains REVERT: P 71 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6978 (ttm110) REVERT: P 110 GLN cc_start: 0.6434 (pt0) cc_final: 0.6179 (pt0) REVERT: P 154 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: P 396 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6184 (tm-30) REVERT: P 431 ASN cc_start: 0.7992 (m110) cc_final: 0.7363 (t0) REVERT: P 454 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6925 (ptm-80) REVERT: P 457 ASN cc_start: 0.6221 (m110) cc_final: 0.5207 (m110) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.1304 time to fit residues: 11.0083 Evaluate side-chains 67 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 205 VAL Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.210860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.197267 restraints weight = 5077.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.200025 restraints weight = 2990.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.201806 restraints weight = 1980.532| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6035 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= 0.173 Angle : 0.724 13.580 4286 Z= 0.371 Chirality : 0.043 0.142 504 Planarity : 0.006 0.082 564 Dihedral : 6.255 22.558 459 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.92 % Favored : 85.38 % Rotamer: Outliers : 6.36 % Allowed : 23.67 % 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 (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: -3.95 (0.35), residues: 431 helix: -1.07 (0.71), residues: 52 sheet: -0.13 (1.16), residues: 28 loop : -3.44 (0.28), residues: 351 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 0.011 0.002 PHE P 373 TYR 0.011 0.002 TYR P 83 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: 1065.80 seconds wall clock time: 19 minutes 31.82 seconds (1171.82 seconds total)