Starting phenix.real_space_refine on Wed Oct 9 14:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrs_18625/10_2024/8qrs_18625.cif" } resolution = 2.86 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= 1.000 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 2034 2.51 5 N 504 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3093 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 16, 'TRANS': 398} Chain breaks: 2 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.88 Number of scatterers: 3093 At special positions: 0 Unit cell: (60.192, 69.388, 71.896, 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 540 8.00 N 504 7.00 C 2034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 418.6 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 86.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.591A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 118 Proline residue: B 83 - end of helix removed outlier: 3.589A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.501A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 155 through 158 removed outlier: 4.320A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.606A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 291 removed outlier: 3.677A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 319 removed outlier: 5.478A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.747A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.594A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.501A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) Proline residue: B 380 - end of helix removed outlier: 3.909A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.849A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.824A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209 256 hydrogen bonds defined for protein. 765 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: 0.88 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 978 1.34 - 1.46: 649 1.46 - 1.58: 1497 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3148 Sorted by residual: bond pdb=" N GLN B 601 " pdb=" CA GLN B 601 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N LEU B 49 " pdb=" CA LEU B 49 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C LEU B 105 " pdb=" O LEU B 105 " ideal model delta sigma weight residual 1.238 1.245 -0.008 1.28e-02 6.10e+03 3.58e-01 bond pdb=" CA GLN B 154 " pdb=" C GLN B 154 " ideal model delta sigma weight residual 1.524 1.531 -0.008 1.26e-02 6.30e+03 3.56e-01 bond pdb=" C LEU B 379 " pdb=" O LEU B 379 " ideal model delta sigma weight residual 1.244 1.238 0.006 1.00e-02 1.00e+04 3.46e-01 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 4028 0.90 - 1.80: 193 1.80 - 2.70: 44 2.70 - 3.59: 13 3.59 - 4.49: 10 Bond angle restraints: 4288 Sorted by residual: angle pdb=" C VAL B 222 " pdb=" N GLY B 223 " pdb=" CA GLY B 223 " ideal model delta sigma weight residual 122.66 120.59 2.07 9.80e-01 1.04e+00 4.48e+00 angle pdb=" N VAL B 72 " pdb=" CA VAL B 72 " pdb=" C VAL B 72 " ideal model delta sigma weight residual 111.00 109.08 1.92 1.09e+00 8.42e-01 3.10e+00 angle pdb=" N GLY B 223 " pdb=" CA GLY B 223 " pdb=" C GLY B 223 " ideal model delta sigma weight residual 111.12 114.01 -2.89 1.89e+00 2.80e-01 2.34e+00 angle pdb=" N VAL B 450 " pdb=" CA VAL B 450 " pdb=" CB VAL B 450 " ideal model delta sigma weight residual 112.07 109.81 2.26 1.52e+00 4.33e-01 2.21e+00 angle pdb=" C ASP B 294 " pdb=" N VAL B 295 " pdb=" CA VAL B 295 " ideal model delta sigma weight residual 120.56 122.41 -1.85 1.26e+00 6.30e-01 2.17e+00 ... (remaining 4283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.25: 1624 13.25 - 26.50: 158 26.50 - 39.74: 41 39.74 - 52.99: 16 52.99 - 66.24: 6 Dihedral angle restraints: 1845 sinusoidal: 674 harmonic: 1171 Sorted by residual: dihedral pdb=" CA SER B 73 " pdb=" C SER B 73 " pdb=" N GLY B 74 " pdb=" CA GLY B 74 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 388 " pdb=" CB ASP B 388 " pdb=" CG ASP B 388 " pdb=" OD1 ASP B 388 " ideal model delta sinusoidal sigma weight residual -30.00 -85.01 55.01 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -60.00 -118.31 58.31 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 361 0.026 - 0.053: 96 0.053 - 0.079: 59 0.079 - 0.106: 18 0.106 - 0.132: 4 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL B 222 " pdb=" N VAL B 222 " pdb=" C VAL B 222 " pdb=" CB VAL B 222 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 535 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 342 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO B 343 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " -0.175 9.50e-02 1.11e+02 7.85e-02 3.99e+00 pdb=" NE ARG B 126 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " -0.137 9.50e-02 1.11e+02 6.18e-02 2.66e+00 pdb=" NE ARG B 335 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.002 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 395 2.75 - 3.28: 3293 3.28 - 3.82: 5498 3.82 - 4.36: 6072 4.36 - 4.90: 10911 Nonbonded interactions: 26169 Sorted by model distance: nonbonded pdb=" OE1 GLN B 394 " pdb=" OG SER B 424 " model vdw 2.208 3.040 nonbonded pdb=" O THR B 350 " pdb=" OG SER B 351 " model vdw 2.236 3.040 nonbonded pdb=" O LEU B 318 " pdb=" OH TYR B 334 " model vdw 2.244 3.040 nonbonded pdb=" CD2 LEU B 284 " pdb=" CE LYS B 288 " model vdw 2.317 3.860 nonbonded pdb=" O THR B 416 " pdb=" OG1 THR B 420 " model vdw 2.369 3.040 ... (remaining 26164 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.003 0.032 3148 Z= 0.169 Angle : 0.531 4.493 4288 Z= 0.299 Chirality : 0.035 0.132 538 Planarity : 0.006 0.078 530 Dihedral : 12.975 66.238 1093 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 11.62 % Favored : 88.07 % 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: 1.87 (0.43), residues: 409 helix: 1.59 (0.29), residues: 340 sheet: -1.52 (1.31), residues: 20 loop : 0.37 (0.94), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.002 0.001 HIS B 373 PHE 0.009 0.001 PHE B 299 TYR 0.007 0.001 TYR B 208 ARG 0.010 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.359 Fit side-chains REVERT: B 85 ARG cc_start: 0.7368 (mtt180) cc_final: 0.5853 (tmt170) REVERT: B 247 LYS cc_start: 0.7660 (mttt) cc_final: 0.7204 (mtpm) REVERT: B 301 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7130 (ttt180) REVERT: B 362 LYS cc_start: 0.7990 (tttt) cc_final: 0.7669 (tttp) REVERT: B 407 GLN cc_start: 0.8182 (mt0) cc_final: 0.7976 (mp10) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 1.1199 time to fit residues: 56.7423 Evaluate side-chains 46 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3148 Z= 0.187 Angle : 0.537 6.856 4288 Z= 0.264 Chirality : 0.037 0.136 538 Planarity : 0.005 0.042 530 Dihedral : 4.038 37.704 437 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.45 % Allowed : 11.31 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.42), residues: 409 helix: 2.26 (0.28), residues: 338 sheet: -1.78 (1.29), residues: 20 loop : -0.13 (0.92), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.011 0.001 PHE B 336 TYR 0.007 0.001 TYR B 208 ARG 0.005 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.431 Fit side-chains REVERT: B 85 ARG cc_start: 0.7336 (mtt180) cc_final: 0.5786 (tmt170) REVERT: B 247 LYS cc_start: 0.7638 (mttt) cc_final: 0.7197 (mtpm) REVERT: B 301 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7073 (ttt180) REVERT: B 362 LYS cc_start: 0.8058 (tttt) cc_final: 0.7763 (tttp) REVERT: B 387 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7248 (mtt) REVERT: B 407 GLN cc_start: 0.8164 (mt0) cc_final: 0.7885 (mp10) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 1.1073 time to fit residues: 55.2613 Evaluate side-chains 42 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.198 Angle : 0.516 6.815 4288 Z= 0.253 Chirality : 0.037 0.142 538 Planarity : 0.004 0.035 530 Dihedral : 4.090 40.281 437 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.98 % Allowed : 11.62 % Favored : 84.40 % 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: 3.02 (0.43), residues: 409 helix: 2.41 (0.28), residues: 338 sheet: -1.76 (1.26), residues: 20 loop : 0.90 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.005 0.001 TYR B 276 ARG 0.005 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.334 Fit side-chains REVERT: B 85 ARG cc_start: 0.7373 (mtt180) cc_final: 0.5814 (tmt170) REVERT: B 247 LYS cc_start: 0.7646 (mttt) cc_final: 0.7203 (mtpm) REVERT: B 301 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7084 (ttt180) REVERT: B 362 LYS cc_start: 0.8034 (tttt) cc_final: 0.7770 (tttp) REVERT: B 387 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7268 (mtt) REVERT: B 407 GLN cc_start: 0.8171 (mt0) cc_final: 0.7865 (mt0) outliers start: 13 outliers final: 6 residues processed: 49 average time/residue: 1.1196 time to fit residues: 56.9667 Evaluate side-chains 45 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3148 Z= 0.206 Angle : 0.516 7.041 4288 Z= 0.249 Chirality : 0.037 0.145 538 Planarity : 0.004 0.033 530 Dihedral : 4.127 45.221 437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.98 % Allowed : 12.84 % Favored : 83.18 % 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: 3.08 (0.43), residues: 409 helix: 2.46 (0.28), residues: 338 sheet: -1.63 (1.25), residues: 20 loop : 0.82 (0.96), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.001 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.006 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8236 (tt) cc_final: 0.8031 (tm) REVERT: B 85 ARG cc_start: 0.7343 (mtt180) cc_final: 0.5663 (tmt170) REVERT: B 247 LYS cc_start: 0.7650 (mttt) cc_final: 0.7209 (mtpm) REVERT: B 301 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7100 (ttt180) REVERT: B 362 LYS cc_start: 0.8027 (tttt) cc_final: 0.7768 (tttp) REVERT: B 387 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7249 (mtt) REVERT: B 407 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: B 446 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7364 (m) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 1.1877 time to fit residues: 57.7437 Evaluate side-chains 51 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3148 Z= 0.151 Angle : 0.488 7.309 4288 Z= 0.237 Chirality : 0.036 0.148 538 Planarity : 0.004 0.035 530 Dihedral : 4.235 51.955 437 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.36 % Allowed : 14.68 % Favored : 81.96 % 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: 3.24 (0.42), residues: 409 helix: 2.53 (0.28), residues: 341 sheet: -1.64 (1.24), residues: 20 loop : 1.09 (0.91), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.007 0.001 PHE B 336 TYR 0.003 0.001 TYR B 334 ARG 0.005 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8206 (tt) cc_final: 0.7986 (tm) REVERT: B 247 LYS cc_start: 0.7621 (mttt) cc_final: 0.7178 (mtpm) REVERT: B 267 MET cc_start: 0.8084 (mmm) cc_final: 0.7767 (mtt) REVERT: B 301 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7072 (ttt180) REVERT: B 362 LYS cc_start: 0.8002 (tttt) cc_final: 0.7767 (tttp) REVERT: B 387 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: B 407 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: B 446 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7272 (m) outliers start: 11 outliers final: 2 residues processed: 51 average time/residue: 1.1241 time to fit residues: 59.2646 Evaluate side-chains 46 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3148 Z= 0.195 Angle : 0.500 7.434 4288 Z= 0.242 Chirality : 0.037 0.144 538 Planarity : 0.004 0.035 530 Dihedral : 4.418 58.669 437 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.36 % Allowed : 16.21 % Favored : 80.43 % 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: 3.20 (0.42), residues: 409 helix: 2.52 (0.28), residues: 341 sheet: -1.68 (1.25), residues: 20 loop : 0.93 (0.88), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.001 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.003 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7653 (mttt) cc_final: 0.7216 (mtpm) REVERT: B 267 MET cc_start: 0.8105 (mmm) cc_final: 0.7890 (mtt) REVERT: B 292 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7020 (ptp) REVERT: B 301 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7103 (ttt180) REVERT: B 362 LYS cc_start: 0.8003 (tttt) cc_final: 0.7767 (tttp) REVERT: B 387 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7258 (mtt) REVERT: B 407 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: B 446 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7288 (m) REVERT: B 475 ASP cc_start: 0.7113 (m-30) cc_final: 0.6890 (m-30) outliers start: 11 outliers final: 3 residues processed: 49 average time/residue: 1.0805 time to fit residues: 54.8084 Evaluate side-chains 50 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3148 Z= 0.228 Angle : 0.532 8.630 4288 Z= 0.254 Chirality : 0.037 0.143 538 Planarity : 0.004 0.035 530 Dihedral : 4.392 56.265 437 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.67 % Allowed : 16.82 % Favored : 79.51 % 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: 3.09 (0.42), residues: 409 helix: 2.45 (0.28), residues: 341 sheet: -1.74 (1.24), residues: 20 loop : 0.93 (0.89), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7682 (mttt) cc_final: 0.7250 (mtpm) REVERT: B 292 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7068 (ptp) REVERT: B 301 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7155 (ttt180) REVERT: B 362 LYS cc_start: 0.8019 (tttt) cc_final: 0.7773 (tttp) REVERT: B 387 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7311 (mtt) REVERT: B 407 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: B 446 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7323 (m) outliers start: 12 outliers final: 3 residues processed: 47 average time/residue: 1.1014 time to fit residues: 53.5942 Evaluate side-chains 48 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3148 Z= 0.152 Angle : 0.502 8.665 4288 Z= 0.237 Chirality : 0.036 0.145 538 Planarity : 0.004 0.035 530 Dihedral : 4.244 53.332 437 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.45 % Allowed : 16.21 % Favored : 81.35 % 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: 3.28 (0.42), residues: 409 helix: 2.59 (0.28), residues: 341 sheet: -1.50 (1.29), residues: 20 loop : 0.76 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 PHE 0.007 0.001 PHE B 336 TYR 0.005 0.001 TYR B 208 ARG 0.004 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7677 (mttt) cc_final: 0.7243 (mtpm) REVERT: B 301 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7150 (ttt180) REVERT: B 362 LYS cc_start: 0.7961 (tttt) cc_final: 0.7759 (tttp) REVERT: B 387 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7213 (mtt) REVERT: B 407 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: B 446 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7197 (m) REVERT: B 454 SER cc_start: 0.8361 (m) cc_final: 0.8044 (p) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.9920 time to fit residues: 49.3478 Evaluate side-chains 47 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3148 Z= 0.198 Angle : 0.515 8.069 4288 Z= 0.245 Chirality : 0.037 0.142 538 Planarity : 0.004 0.035 530 Dihedral : 3.430 11.523 435 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.45 % Allowed : 16.82 % Favored : 80.73 % 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: 3.24 (0.41), residues: 409 helix: 2.56 (0.27), residues: 341 sheet: -1.59 (1.27), residues: 20 loop : 0.80 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7671 (mttt) cc_final: 0.7239 (mtpm) REVERT: B 301 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7132 (ttt180) REVERT: B 362 LYS cc_start: 0.7994 (tttt) cc_final: 0.7772 (tttp) REVERT: B 387 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7257 (mtt) REVERT: B 407 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: B 446 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7195 (m) REVERT: B 454 SER cc_start: 0.8332 (m) cc_final: 0.8013 (p) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 1.1293 time to fit residues: 56.0449 Evaluate side-chains 46 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.175 Angle : 0.510 8.587 4288 Z= 0.241 Chirality : 0.036 0.138 538 Planarity : 0.004 0.035 530 Dihedral : 3.390 11.516 435 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.83 % Allowed : 17.43 % Favored : 80.73 % 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: 3.30 (0.41), residues: 409 helix: 2.61 (0.27), residues: 341 sheet: -1.59 (1.28), residues: 20 loop : 0.77 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.008 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 247 LYS cc_start: 0.7668 (mttt) cc_final: 0.7236 (mtpm) REVERT: B 301 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7142 (ttt180) REVERT: B 362 LYS cc_start: 0.7976 (tttt) cc_final: 0.7773 (tttp) REVERT: B 387 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7239 (mtt) REVERT: B 446 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7192 (m) REVERT: B 454 SER cc_start: 0.8352 (m) cc_final: 0.8041 (p) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 1.0037 time to fit residues: 47.0063 Evaluate side-chains 44 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0170 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098708 restraints weight = 4015.300| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.10 r_work: 0.3002 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3148 Z= 0.167 Angle : 0.505 8.166 4288 Z= 0.239 Chirality : 0.036 0.144 538 Planarity : 0.004 0.035 530 Dihedral : 3.400 11.785 435 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.14 % Allowed : 17.13 % Favored : 80.73 % 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: 3.38 (0.42), residues: 409 helix: 2.63 (0.28), residues: 342 sheet: -1.49 (1.30), residues: 20 loop : 0.93 (0.85), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.008 0.001 PHE B 237 TYR 0.005 0.001 TYR B 334 ARG 0.004 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.48 seconds wall clock time: 31 minutes 23.96 seconds (1883.96 seconds total)