Starting phenix.real_space_refine on Fri Apr 5 12:39:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggi_40009/04_2024/8ggi_40009_updated.pdb" } resolution = 3.5 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= 0.025 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 15 5.16 5 C 1470 2.51 5 N 348 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 122": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2203 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.86, per 1000 atoms: 0.84 Number of scatterers: 2203 At special positions: 0 Unit cell: (54.6651, 83.2992, 63.3421, 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 15 16.00 O 370 8.00 N 348 7.00 C 1470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=1.41 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: 0.90 Conformation dependent library (CDL) restraints added in 461.4 milliseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.770A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 96 removed outlier: 4.624A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 135 removed outlier: 3.756A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 164 removed outlier: 3.657A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.686A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 237 removed outlier: 3.953A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE R 223 " --> pdb=" O TYR R 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 279 Processing helix chain 'R' and resid 287 through 298 removed outlier: 3.692A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.569A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 339 133 hydrogen bonds defined for protein. 399 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: 0.49 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: 1.22 - 1.34: 651 1.34 - 1.46: 581 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.83: 21 Bond restraints: 2257 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.567 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C CYS R 191 " pdb=" O CYS R 191 " ideal model delta sigma weight residual 1.235 1.220 0.015 7.50e-03 1.78e+04 4.18e+00 ... (remaining 2252 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.40: 63 107.40 - 114.06: 1318 114.06 - 120.71: 1006 120.71 - 127.37: 673 127.37 - 134.02: 27 Bond angle restraints: 3087 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 114.04 104.66 9.38 1.24e+00 6.50e-01 5.73e+01 angle pdb=" N PHE R 193 " pdb=" CA PHE R 193 " pdb=" C PHE R 193 " ideal model delta sigma weight residual 108.67 116.73 -8.06 1.55e+00 4.16e-01 2.70e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" C CYS R 191 " ideal model delta sigma weight residual 113.21 106.63 6.58 1.40e+00 5.10e-01 2.21e+01 angle pdb=" N CYS R 190 " pdb=" CA CYS R 190 " pdb=" C CYS R 190 " ideal model delta sigma weight residual 109.96 115.88 -5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sigma weight residual 110.65 115.26 -4.61 1.71e+00 3.42e-01 7.28e+00 ... (remaining 3082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 1151 16.08 - 32.17: 122 32.17 - 48.25: 25 48.25 - 64.33: 3 64.33 - 80.42: 3 Dihedral angle restraints: 1304 sinusoidal: 467 harmonic: 837 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER R 207 " pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta harmonic sigma weight residual -180.00 -164.16 -15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CB MET R 171 " pdb=" CG MET R 171 " pdb=" SD MET R 171 " pdb=" CE MET R 171 " ideal model delta sinusoidal sigma weight residual 60.00 117.75 -57.75 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 232 0.033 - 0.066: 102 0.066 - 0.098: 33 0.098 - 0.131: 10 0.131 - 0.164: 1 Chirality restraints: 378 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO R 88 " pdb=" N PRO R 88 " pdb=" C PRO R 88 " pdb=" CB PRO R 88 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 375 not shown) Planarity restraints: 368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 190 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C CYS R 190 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS R 190 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 191 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 237 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" CD GLU R 237 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU R 237 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU R 237 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.006 2.00e-02 2.50e+03 7.40e-03 1.37e+00 pdb=" CG TRP R 313 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.000 2.00e-02 2.50e+03 ... (remaining 365 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 445 2.77 - 3.31: 2116 3.31 - 3.84: 3512 3.84 - 4.37: 3721 4.37 - 4.90: 6791 Nonbonded interactions: 16585 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.242 2.440 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.333 2.520 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.407 2.440 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.450 2.440 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.495 2.520 ... (remaining 16580 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: 1.440 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: 7.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 0.053 2257 Z= 0.253 Angle : 0.692 9.382 3087 Z= 0.389 Chirality : 0.042 0.164 378 Planarity : 0.004 0.030 368 Dihedral : 13.755 80.416 754 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.47 (0.51), residues: 280 helix: 1.60 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -0.70 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 313 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 193 TYR 0.007 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.245 Fit side-chains REVERT: R 82 MET cc_start: 0.8318 (ttm) cc_final: 0.8052 (ttm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1652 time to fit residues: 8.3968 Evaluate side-chains 34 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2257 Z= 0.202 Angle : 0.495 6.927 3087 Z= 0.259 Chirality : 0.039 0.107 378 Planarity : 0.003 0.026 368 Dihedral : 4.507 20.235 316 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 8.00 % Favored : 90.22 % 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: 1.60 (0.51), residues: 280 helix: 1.67 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -0.75 (0.78), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.008 0.001 PHE R 332 TYR 0.008 0.001 TYR R 316 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.242 Fit side-chains REVERT: R 279 MET cc_start: 0.8591 (mmm) cc_final: 0.8305 (mmm) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.1599 time to fit residues: 7.2254 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2257 Z= 0.206 Angle : 0.484 7.536 3087 Z= 0.251 Chirality : 0.039 0.106 378 Planarity : 0.003 0.026 368 Dihedral : 4.418 17.148 316 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.78 % Allowed : 8.89 % Favored : 89.33 % 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: 1.51 (0.51), residues: 280 helix: 1.58 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -0.88 (0.74), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.007 0.001 PHE R 332 TYR 0.007 0.001 TYR R 132 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: R 279 MET cc_start: 0.8573 (mmm) cc_final: 0.8286 (mmm) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1620 time to fit residues: 7.1347 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2257 Z= 0.182 Angle : 0.484 9.857 3087 Z= 0.245 Chirality : 0.038 0.107 378 Planarity : 0.003 0.026 368 Dihedral : 4.286 16.838 316 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.89 % Allowed : 12.89 % Favored : 86.22 % 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: 1.53 (0.51), residues: 280 helix: 1.61 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -0.95 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.006 0.001 PHE R 332 TYR 0.008 0.001 TYR R 132 ARG 0.004 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: R 279 MET cc_start: 0.8603 (mmm) cc_final: 0.8318 (mmm) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1777 time to fit residues: 7.8487 Evaluate side-chains 35 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2257 Z= 0.247 Angle : 0.506 8.951 3087 Z= 0.261 Chirality : 0.039 0.109 378 Planarity : 0.003 0.027 368 Dihedral : 4.339 16.857 316 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.67 % Allowed : 12.00 % Favored : 85.33 % 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: 1.46 (0.50), residues: 280 helix: 1.63 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.05 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 332 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.259 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.1840 time to fit residues: 7.8613 Evaluate side-chains 36 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2257 Z= 0.213 Angle : 0.487 8.051 3087 Z= 0.251 Chirality : 0.039 0.107 378 Planarity : 0.003 0.027 368 Dihedral : 4.258 17.039 316 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.89 % Allowed : 13.33 % Favored : 85.78 % 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: 1.45 (0.51), residues: 280 helix: 1.64 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.13 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.006 0.001 PHE R 332 TYR 0.008 0.001 TYR R 132 ARG 0.004 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.232 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1945 time to fit residues: 7.5945 Evaluate side-chains 34 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2257 Z= 0.182 Angle : 0.480 8.625 3087 Z= 0.245 Chirality : 0.039 0.105 378 Planarity : 0.003 0.027 368 Dihedral : 4.234 17.084 316 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.44 % Allowed : 14.67 % Favored : 84.89 % 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: 1.49 (0.50), residues: 280 helix: 1.66 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.21 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.006 0.001 PHE R 332 TYR 0.007 0.001 TYR R 132 ARG 0.005 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.223 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1988 time to fit residues: 7.7403 Evaluate side-chains 34 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2257 Z= 0.226 Angle : 0.499 8.839 3087 Z= 0.254 Chirality : 0.039 0.106 378 Planarity : 0.003 0.027 368 Dihedral : 4.310 17.021 316 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 14.22 % Favored : 84.44 % 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: 1.49 (0.50), residues: 280 helix: 1.64 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.17 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.006 0.001 PHE R 332 TYR 0.008 0.001 TYR R 132 ARG 0.006 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.251 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1910 time to fit residues: 7.9399 Evaluate side-chains 34 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2257 Z= 0.213 Angle : 0.502 9.133 3087 Z= 0.254 Chirality : 0.039 0.107 378 Planarity : 0.003 0.030 368 Dihedral : 4.343 17.049 316 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.89 % Allowed : 13.78 % Favored : 85.33 % 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: 1.50 (0.51), residues: 280 helix: 1.66 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.18 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.006 0.001 PHE R 332 TYR 0.010 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.260 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.2053 time to fit residues: 7.5542 Evaluate side-chains 33 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2257 Z= 0.202 Angle : 0.497 9.030 3087 Z= 0.252 Chirality : 0.039 0.106 378 Planarity : 0.003 0.032 368 Dihedral : 4.338 17.033 316 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.89 % Allowed : 13.78 % Favored : 85.33 % 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: 1.49 (0.51), residues: 280 helix: 1.64 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.17 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.006 0.001 PHE R 332 TYR 0.010 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.237 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1982 time to fit residues: 7.7535 Evaluate side-chains 34 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.0010 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.097429 restraints weight = 2998.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099813 restraints weight = 1716.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101437 restraints weight = 1211.194| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2257 Z= 0.166 Angle : 0.474 8.759 3087 Z= 0.240 Chirality : 0.038 0.105 378 Planarity : 0.003 0.031 368 Dihedral : 4.181 17.111 316 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.89 % Allowed : 13.78 % Favored : 85.33 % 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: 1.61 (0.51), residues: 280 helix: 1.69 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -1.07 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.005 0.001 PHE R 290 TYR 0.008 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 970.60 seconds wall clock time: 18 minutes 4.53 seconds (1084.53 seconds total)