Starting phenix.real_space_refine on Sun Mar 10 15:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwf_20922/03_2024/6uwf_20922_updated.pdb" } resolution = 3.08 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= 0.002 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 P 2 5.49 5 S 18 5.16 5 C 2096 2.51 5 N 502 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3178 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3178 Unusual residues: {'6OU': 2} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 417, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 398, None: 2} Not linked: pdbres="ASP A 501 " pdbres="6OU A 502 " Not linked: pdbres="6OU A 502 " pdbres="6OU A 503 " Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'FME:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.38, per 1000 atoms: 0.75 Number of scatterers: 3178 At special positions: 0 Unit cell: (71.02, 67.84, 81.62, 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) S 18 16.00 P 2 15.00 O 560 8.00 N 502 7.00 C 2096 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 663.4 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 12 through 32 removed outlier: 3.883A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 68 removed outlier: 4.237A pdb=" N LEU A 49 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 58 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N MET A 59 " --> pdb=" O MET A 56 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 4.469A pdb=" N PHE A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA A 64 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 65 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 removed outlier: 3.630A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.586A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.645A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.617A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 244 removed outlier: 4.478A pdb=" N VAL A 237 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 258 through 275 removed outlier: 5.780A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.264A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.545A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.725A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.331A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.818A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 415 removed outlier: 4.063A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 507 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: 0.77 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 488 1.31 - 1.43: 788 1.43 - 1.56: 1894 1.56 - 1.68: 31 1.68 - 1.80: 35 Bond restraints: 3236 Sorted by residual: bond pdb=" C16 6OU A 502 " pdb=" O18 6OU A 502 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C16 6OU A 503 " pdb=" O18 6OU A 503 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C31 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C31 6OU A 503 " pdb=" O30 6OU A 503 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C39 6OU A 502 " pdb=" C40 6OU A 502 " ideal model delta sigma weight residual 1.497 1.569 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 3231 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.54: 101 106.54 - 113.32: 1856 113.32 - 120.11: 1179 120.11 - 126.89: 1229 126.89 - 133.67: 29 Bond angle restraints: 4394 Sorted by residual: angle pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " pdb=" O26 6OU A 502 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 108.18 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.48e+01 angle pdb=" N LEU A 374 " pdb=" CA LEU A 374 " pdb=" C LEU A 374 " ideal model delta sigma weight residual 113.17 108.81 4.36 1.26e+00 6.30e-01 1.20e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 119.66 -5.76 1.80e+00 3.09e-01 1.03e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 1842 28.42 - 56.85: 65 56.85 - 85.27: 10 85.27 - 113.70: 2 113.70 - 142.12: 3 Dihedral angle restraints: 1922 sinusoidal: 739 harmonic: 1183 Sorted by residual: dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N PHE A 122 " pdb=" CA PHE A 122 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C37 6OU A 503 " pdb=" C38 6OU A 503 " pdb=" C39 6OU A 503 " pdb=" C40 6OU A 503 " ideal model delta sinusoidal sigma weight residual 178.01 -39.87 -142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C09 6OU A 503 " pdb=" C10 6OU A 503 " pdb=" C11 6OU A 503 " pdb=" C12 6OU A 503 " ideal model delta sinusoidal sigma weight residual 179.71 -48.47 -131.82 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 1919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 368 0.046 - 0.092: 134 0.092 - 0.137: 29 0.137 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 541 Sorted by residual: chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.82 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 538 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 45 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 153 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 206 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.030 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 910 2.82 - 3.34: 3043 3.34 - 3.86: 5341 3.86 - 4.38: 6311 4.38 - 4.90: 10748 Nonbonded interactions: 26353 Sorted by model distance: nonbonded pdb=" O ALA A 360 " pdb=" OH TYR A 383 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.321 2.440 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.325 2.440 nonbonded pdb=" O THR A 340 " pdb=" OG1 THR A 344 " model vdw 2.336 2.440 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.345 2.440 ... (remaining 26348 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 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.410 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.008 0.088 3236 Z= 0.493 Angle : 1.079 15.348 4394 Z= 0.513 Chirality : 0.049 0.229 541 Planarity : 0.008 0.054 537 Dihedral : 17.111 142.124 1172 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: -3.86 (0.32), residues: 413 helix: -2.35 (0.20), residues: 338 sheet: None (None), residues: 0 loop : -2.27 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.015 0.002 PHE A 157 TYR 0.029 0.003 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.319 Fit side-chains REVERT: A 327 ASN cc_start: 0.8784 (m110) cc_final: 0.8305 (m-40) REVERT: A 362 MET cc_start: 0.9011 (tpp) cc_final: 0.8494 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1052 time to fit residues: 6.8383 Evaluate side-chains 41 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3236 Z= 0.230 Angle : 0.564 5.588 4394 Z= 0.285 Chirality : 0.038 0.144 541 Planarity : 0.005 0.031 537 Dihedral : 15.593 125.262 508 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.31 % Allowed : 11.38 % Favored : 88.31 % 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: -1.33 (0.40), residues: 413 helix: -0.48 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -2.00 (0.66), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.009 0.001 PHE A 157 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.359 Fit side-chains REVERT: A 323 PHE cc_start: 0.8886 (m-80) cc_final: 0.8526 (m-80) REVERT: A 327 ASN cc_start: 0.8881 (m110) cc_final: 0.8286 (m-40) REVERT: A 362 MET cc_start: 0.9056 (tpp) cc_final: 0.8585 (tpt) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.1026 time to fit residues: 6.0367 Evaluate side-chains 40 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 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: 0.8265 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3236 Z= 0.254 Angle : 0.553 5.473 4394 Z= 0.275 Chirality : 0.039 0.139 541 Planarity : 0.004 0.029 537 Dihedral : 14.891 116.704 508 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.23 % Allowed : 11.69 % Favored : 87.08 % 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: -0.59 (0.41), residues: 413 helix: 0.03 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.74 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.306 Fit side-chains REVERT: A 37 HIS cc_start: 0.7298 (t70) cc_final: 0.6992 (t70) REVERT: A 327 ASN cc_start: 0.8886 (m110) cc_final: 0.8571 (m110) REVERT: A 362 MET cc_start: 0.9089 (tpp) cc_final: 0.8644 (tpt) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.0976 time to fit residues: 5.9536 Evaluate side-chains 44 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3236 Z= 0.250 Angle : 0.548 5.432 4394 Z= 0.272 Chirality : 0.039 0.133 541 Planarity : 0.004 0.029 537 Dihedral : 14.498 110.804 508 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 11.69 % Favored : 85.54 % 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: -0.14 (0.42), residues: 413 helix: 0.33 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.49 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.016 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.350 Fit side-chains REVERT: A 37 HIS cc_start: 0.7303 (t70) cc_final: 0.6998 (t70) REVERT: A 327 ASN cc_start: 0.8886 (m110) cc_final: 0.8576 (m110) REVERT: A 362 MET cc_start: 0.9087 (tpp) cc_final: 0.8660 (tpt) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1004 time to fit residues: 6.3081 Evaluate side-chains 44 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3236 Z= 0.288 Angle : 0.562 5.440 4394 Z= 0.278 Chirality : 0.040 0.130 541 Planarity : 0.004 0.030 537 Dihedral : 14.453 110.796 508 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.46 % Allowed : 12.92 % Favored : 84.62 % 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: 0.17 (0.42), residues: 413 helix: 0.57 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.32 (0.66), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.011 0.001 PHE A 157 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.331 Fit side-chains REVERT: A 37 HIS cc_start: 0.7330 (t70) cc_final: 0.7032 (t70) REVERT: A 327 ASN cc_start: 0.8880 (m110) cc_final: 0.8261 (m-40) REVERT: A 362 MET cc_start: 0.9068 (tpp) cc_final: 0.8656 (tpt) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1052 time to fit residues: 6.4379 Evaluate side-chains 46 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3236 Z= 0.209 Angle : 0.524 5.340 4394 Z= 0.259 Chirality : 0.038 0.125 541 Planarity : 0.004 0.028 537 Dihedral : 13.988 104.846 508 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % 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: 0.44 (0.42), residues: 413 helix: 0.76 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.23 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.009 0.001 PHE A 157 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.342 Fit side-chains REVERT: A 37 HIS cc_start: 0.7273 (t70) cc_final: 0.6975 (t70) REVERT: A 327 ASN cc_start: 0.8875 (m110) cc_final: 0.8288 (m-40) REVERT: A 362 MET cc_start: 0.9105 (tpp) cc_final: 0.8701 (tpt) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.0970 time to fit residues: 6.3421 Evaluate side-chains 49 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3236 Z= 0.187 Angle : 0.518 5.403 4394 Z= 0.253 Chirality : 0.038 0.121 541 Planarity : 0.004 0.028 537 Dihedral : 13.070 97.119 508 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 14.15 % Favored : 82.77 % 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: 0.69 (0.43), residues: 413 helix: 0.94 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.15 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.009 0.001 PHE A 157 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.344 Fit side-chains REVERT: A 37 HIS cc_start: 0.7266 (t70) cc_final: 0.6955 (t70) REVERT: A 327 ASN cc_start: 0.8859 (m110) cc_final: 0.8321 (m-40) REVERT: A 362 MET cc_start: 0.9111 (tpp) cc_final: 0.8701 (tpt) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.0948 time to fit residues: 6.4325 Evaluate side-chains 47 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 37 optimal weight: 0.0010 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 overall best weight: 0.1398 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3236 Z= 0.118 Angle : 0.490 7.533 4394 Z= 0.237 Chirality : 0.037 0.128 541 Planarity : 0.003 0.026 537 Dihedral : 12.246 84.941 508 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.46 % Allowed : 15.08 % Favored : 82.46 % 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: 1.08 (0.43), residues: 413 helix: 1.14 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -0.79 (0.75), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 132 PHE 0.008 0.001 PHE A 157 TYR 0.011 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.347 Fit side-chains REVERT: A 327 ASN cc_start: 0.8813 (m110) cc_final: 0.8379 (m-40) REVERT: A 362 MET cc_start: 0.9131 (tpp) cc_final: 0.8699 (tpt) outliers start: 8 outliers final: 8 residues processed: 51 average time/residue: 0.0926 time to fit residues: 6.6166 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3236 Z= 0.216 Angle : 0.534 8.729 4394 Z= 0.258 Chirality : 0.038 0.127 541 Planarity : 0.004 0.028 537 Dihedral : 12.169 87.224 508 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 15.38 % Favored : 82.46 % 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: 1.08 (0.43), residues: 413 helix: 1.09 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -0.65 (0.77), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.346 Fit side-chains REVERT: A 37 HIS cc_start: 0.7260 (t70) cc_final: 0.7003 (t70) REVERT: A 327 ASN cc_start: 0.8853 (m110) cc_final: 0.8351 (m-40) REVERT: A 362 MET cc_start: 0.9110 (tpp) cc_final: 0.8667 (tpt) outliers start: 7 outliers final: 7 residues processed: 45 average time/residue: 0.0978 time to fit residues: 6.2255 Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3236 Z= 0.173 Angle : 0.524 9.749 4394 Z= 0.251 Chirality : 0.038 0.124 541 Planarity : 0.004 0.027 537 Dihedral : 11.865 85.246 508 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.46 % Allowed : 15.38 % Favored : 82.15 % 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: 1.12 (0.43), residues: 413 helix: 1.13 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -0.66 (0.77), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.008 0.001 PHE A 157 TYR 0.013 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.379 Fit side-chains REVERT: A 37 HIS cc_start: 0.7270 (t70) cc_final: 0.7013 (t70) REVERT: A 327 ASN cc_start: 0.8850 (m110) cc_final: 0.8369 (m-40) REVERT: A 362 MET cc_start: 0.9123 (tpp) cc_final: 0.8859 (mmm) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0970 time to fit residues: 6.5264 Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.112135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.092260 restraints weight = 4274.835| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.58 r_work: 0.2801 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3236 Z= 0.203 Angle : 0.546 10.268 4394 Z= 0.263 Chirality : 0.038 0.125 541 Planarity : 0.004 0.027 537 Dihedral : 11.738 86.375 508 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.46 % Allowed : 15.69 % Favored : 81.85 % 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: 1.07 (0.43), residues: 413 helix: 1.09 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -0.65 (0.76), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 157 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1110.75 seconds wall clock time: 20 minutes 40.84 seconds (1240.84 seconds total)