Starting phenix.real_space_refine on Tue Feb 13 22:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uk5_26575/02_2024/7uk5_26575.pdb" } resolution = 2.76 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= 0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 346": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.62, per 1000 atoms: 0.95 Number of scatterers: 8000 At special positions: 0 Unit cell: (116.466, 116.466, 78.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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 - 3.50 Amino acid : False - 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: 3.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.096A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 Processing helix chain 'D' and resid 401 through 424 633 hydrogen bonds defined for protein. 1815 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: 2.05 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 2009 1.46 - 1.58: 3655 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" C GLN C 417 " pdb=" N ARG C 418 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.98e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.60: 156 105.60 - 112.72: 4397 112.72 - 119.84: 2528 119.84 - 126.96: 3974 126.96 - 134.08: 69 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.67e+00 angle pdb=" N THR B 182 " pdb=" CA THR B 182 " pdb=" C THR B 182 " ideal model delta sigma weight residual 113.41 110.51 2.90 1.22e+00 6.72e-01 5.66e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.41 110.53 2.88 1.22e+00 6.72e-01 5.58e+00 angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4400 17.87 - 35.73: 336 35.73 - 53.60: 44 53.60 - 71.47: 4 71.47 - 89.34: 8 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.89 -43.11 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 702 0.027 - 0.055: 352 0.055 - 0.082: 199 0.082 - 0.110: 41 0.110 - 0.137: 26 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN B 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN A 417 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 417 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 418 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN C 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN C 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 418 " 0.019 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 810 2.74 - 3.34: 10002 3.34 - 3.94: 15630 3.94 - 4.54: 21328 4.54 - 5.14: 32150 Nonbonded interactions: 79920 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.139 2.520 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 296 " model vdw 2.139 2.520 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH2 ARG A 296 " model vdw 2.139 2.520 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 296 " model vdw 2.139 2.520 nonbonded pdb=" O PHE D 257 " pdb=" OG SER D 260 " model vdw 2.343 2.440 ... (remaining 79915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 11.600 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.960 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.004 0.029 8188 Z= 0.280 Angle : 0.581 4.978 11124 Z= 0.349 Chirality : 0.042 0.137 1320 Planarity : 0.006 0.049 1360 Dihedral : 12.964 89.336 2840 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.27), residues: 1028 helix: 1.57 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 172 HIS 0.001 0.000 HIS D 306 PHE 0.010 0.001 PHE B 289 TYR 0.020 0.002 TYR D 188 ARG 0.004 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.0963 time to fit residues: 126.4844 Evaluate side-chains 96 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8188 Z= 0.270 Angle : 0.512 4.407 11124 Z= 0.287 Chirality : 0.042 0.131 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.915 16.657 1148 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 7.58 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.27), residues: 1028 helix: 1.87 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.49 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.001 0.000 HIS A 306 PHE 0.012 0.001 PHE D 257 TYR 0.017 0.002 TYR D 188 ARG 0.001 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.850 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 1.1678 time to fit residues: 129.5184 Evaluate side-chains 112 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.0370 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8188 Z= 0.286 Angle : 0.517 4.600 11124 Z= 0.285 Chirality : 0.042 0.132 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.898 16.536 1148 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.66 % Allowed : 9.48 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.27), residues: 1028 helix: 1.97 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.34 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.001 0.000 HIS A 179 PHE 0.012 0.001 PHE A 257 TYR 0.019 0.002 TYR B 188 ARG 0.002 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.997 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 1.1992 time to fit residues: 121.5055 Evaluate side-chains 101 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8188 Z= 0.214 Angle : 0.479 4.495 11124 Z= 0.264 Chirality : 0.040 0.124 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.717 15.449 1148 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.18 % Allowed : 10.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.40 (0.27), residues: 1028 helix: 2.13 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.39 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.000 0.000 HIS D 306 PHE 0.010 0.001 PHE D 257 TYR 0.017 0.002 TYR B 188 ARG 0.001 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.914 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 1.1148 time to fit residues: 119.1146 Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0570 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8188 Z= 0.209 Angle : 0.476 4.498 11124 Z= 0.262 Chirality : 0.040 0.123 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.659 15.108 1148 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 13.27 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.28), residues: 1028 helix: 2.20 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.28 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 172 HIS 0.001 0.000 HIS C 179 PHE 0.009 0.001 PHE D 257 TYR 0.016 0.002 TYR B 188 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.971 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 104 average time/residue: 1.0527 time to fit residues: 117.3050 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8188 Z= 0.220 Angle : 0.486 4.528 11124 Z= 0.266 Chirality : 0.040 0.124 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.674 15.053 1148 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.01 % Allowed : 13.86 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.50 (0.28), residues: 1028 helix: 2.18 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.25 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 172 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE A 257 TYR 0.015 0.001 TYR B 188 ARG 0.001 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.942 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 105 average time/residue: 1.0504 time to fit residues: 118.1845 Evaluate side-chains 109 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.193 Angle : 0.476 4.543 11124 Z= 0.260 Chirality : 0.039 0.121 1320 Planarity : 0.005 0.048 1360 Dihedral : 3.594 14.643 1148 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 14.69 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.55 (0.28), residues: 1028 helix: 2.22 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.24 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 172 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE D 257 TYR 0.014 0.001 TYR B 188 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.939 Fit side-chains REVERT: A 279 MET cc_start: 0.5202 (mtm) cc_final: 0.4880 (ptm) REVERT: B 279 MET cc_start: 0.5253 (mtm) cc_final: 0.4931 (ptm) REVERT: C 279 MET cc_start: 0.5254 (mtm) cc_final: 0.4935 (ptm) REVERT: D 279 MET cc_start: 0.5262 (mtm) cc_final: 0.4947 (ptm) outliers start: 12 outliers final: 12 residues processed: 100 average time/residue: 1.1324 time to fit residues: 120.7049 Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8188 Z= 0.202 Angle : 0.489 5.687 11124 Z= 0.264 Chirality : 0.039 0.121 1320 Planarity : 0.005 0.047 1360 Dihedral : 3.597 14.448 1148 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 14.34 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.28), residues: 1028 helix: 2.21 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.20 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 172 HIS 0.001 0.000 HIS D 179 PHE 0.009 0.001 PHE D 257 TYR 0.013 0.001 TYR D 188 ARG 0.001 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.815 Fit side-chains REVERT: A 279 MET cc_start: 0.5350 (mtm) cc_final: 0.5027 (ptm) REVERT: B 279 MET cc_start: 0.5371 (mtm) cc_final: 0.5095 (ptm) REVERT: C 279 MET cc_start: 0.5376 (mtm) cc_final: 0.5099 (ptm) REVERT: D 279 MET cc_start: 0.5385 (mtm) cc_final: 0.5113 (ptm) outliers start: 12 outliers final: 12 residues processed: 105 average time/residue: 1.0672 time to fit residues: 119.9735 Evaluate side-chains 107 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8188 Z= 0.205 Angle : 0.493 5.809 11124 Z= 0.266 Chirality : 0.040 0.121 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.592 14.596 1148 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 13.63 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.28), residues: 1028 helix: 2.21 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.22 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 172 HIS 0.001 0.000 HIS D 179 PHE 0.009 0.001 PHE A 257 TYR 0.012 0.001 TYR B 188 ARG 0.001 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.936 Fit side-chains REVERT: A 279 MET cc_start: 0.5351 (mtm) cc_final: 0.5112 (ptm) REVERT: B 279 MET cc_start: 0.5348 (mtm) cc_final: 0.5103 (ptm) REVERT: C 279 MET cc_start: 0.5351 (mtm) cc_final: 0.5106 (ptm) REVERT: D 279 MET cc_start: 0.5357 (mtm) cc_final: 0.5120 (ptm) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 1.1288 time to fit residues: 121.9236 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.168 Angle : 0.477 5.590 11124 Z= 0.257 Chirality : 0.039 0.117 1320 Planarity : 0.005 0.048 1360 Dihedral : 3.487 13.938 1148 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.42 % Allowed : 13.74 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.28), residues: 1028 helix: 2.32 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.25 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.001 0.000 HIS B 179 PHE 0.008 0.001 PHE D 257 TYR 0.012 0.001 TYR B 188 ARG 0.000 0.000 ARG A 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.875 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 101 average time/residue: 1.1033 time to fit residues: 119.0218 Evaluate side-chains 104 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.169541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120457 restraints weight = 8683.639| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.87 r_work: 0.3290 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.166 Angle : 0.479 5.899 11124 Z= 0.257 Chirality : 0.039 0.117 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.441 13.074 1148 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.95 % Allowed : 14.22 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.28), residues: 1028 helix: 2.38 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.19 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 362 HIS 0.001 0.000 HIS A 179 PHE 0.008 0.001 PHE A 257 TYR 0.012 0.001 TYR B 188 ARG 0.000 0.000 ARG D 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.51 seconds wall clock time: 52 minutes 13.27 seconds (3133.27 seconds total)