Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:05:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/11_2022/7p9u_13266.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.041 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B GLU 493": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3943 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 375 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3568 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain breaks: 1 Time building chain proxies: 2.82, per 1000 atoms: 0.72 Number of scatterers: 3943 At special positions: 0 Unit cell: (68.224, 81.536, 89.856, 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 22 16.00 O 665 8.00 N 625 7.00 C 2631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 158 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 764.4 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 77.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 178 through 208 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 60 through 63 Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.132A pdb=" N GLY B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 105 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.718A pdb=" N TYR B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.814A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 Processing helix chain 'B' and resid 162 through 183 Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.597A pdb=" N ILE B 190 " --> pdb=" O TRP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 216 removed outlier: 3.523A pdb=" N ILE B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.547A pdb=" N TYR B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 292 removed outlier: 3.941A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 318 through 349 removed outlier: 3.738A pdb=" N SER B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET B 331 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 384 through 413 removed outlier: 3.930A pdb=" N ASN B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 442 removed outlier: 3.626A pdb=" N ALA B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 460 removed outlier: 3.573A pdb=" N THR B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 478 through 493 Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 359 263 hydrogen bonds defined for protein. 762 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: 1.10 Time building geometry restraints manager: 1.65 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: 1179 1.34 - 1.46: 916 1.46 - 1.58: 1914 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4045 Sorted by residual: bond pdb=" CG MET B 243 " pdb=" SD MET B 243 " ideal model delta sigma weight residual 1.803 1.760 0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CG MET B 357 " pdb=" SD MET B 357 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET B 357 " pdb=" CE MET B 357 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CB THR B 169 " pdb=" CG2 THR B 169 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.33e-01 bond pdb=" CA ASP B 446 " pdb=" CB ASP B 446 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.58e-02 4.01e+03 8.08e-01 ... (remaining 4040 not shown) Histogram of bond angle deviations from ideal: 95.00 - 102.81: 23 102.81 - 110.61: 1182 110.61 - 118.41: 1970 118.41 - 126.22: 2261 126.22 - 134.02: 75 Bond angle restraints: 5511 Sorted by residual: angle pdb=" CA LYS B 362 " pdb=" CB LYS B 362 " pdb=" CG LYS B 362 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.19e+00 angle pdb=" C PRO B 262 " pdb=" N GLU B 263 " pdb=" CA GLU B 263 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" CG MET B 357 " pdb=" SD MET B 357 " pdb=" CE MET B 357 " ideal model delta sigma weight residual 100.90 95.00 5.90 2.20e+00 2.07e-01 7.19e+00 angle pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sigma weight residual 113.80 116.39 -2.59 1.00e+00 1.00e+00 6.70e+00 angle pdb=" C PRO B 161 " pdb=" N GLU B 162 " pdb=" CA GLU B 162 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.61e+00 ... (remaining 5506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2090 17.16 - 34.32: 222 34.32 - 51.47: 37 51.47 - 68.63: 5 68.63 - 85.79: 4 Dihedral angle restraints: 2358 sinusoidal: 909 harmonic: 1449 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 158 " pdb=" CB CYS B 158 " ideal model delta sinusoidal sigma weight residual -86.00 -171.79 85.79 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CA ARG A 212 " pdb=" C ARG A 212 " pdb=" N GLU A 213 " pdb=" CA GLU A 213 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS B 362 " pdb=" C LYS B 362 " pdb=" N HIS B 363 " pdb=" CA HIS B 363 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 375 0.030 - 0.060: 181 0.060 - 0.090: 67 0.090 - 0.120: 31 0.120 - 0.150: 5 Chirality restraints: 659 Sorted by residual: chirality pdb=" CB THR B 169 " pdb=" CA THR B 169 " pdb=" OG1 THR B 169 " pdb=" CG2 THR B 169 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ASP B 446 " pdb=" N ASP B 446 " pdb=" C ASP B 446 " pdb=" CB ASP B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA VAL B 495 " pdb=" N VAL B 495 " pdb=" C VAL B 495 " pdb=" CB VAL B 495 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 656 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 249 " 0.020 2.00e-02 2.50e+03 2.45e-02 1.50e+01 pdb=" CG TRP B 249 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 249 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 249 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 249 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 249 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 249 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 249 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 249 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 249 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 239 " -0.020 2.00e-02 2.50e+03 1.30e-02 2.95e+00 pdb=" CG PHE B 239 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 239 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 239 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 239 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 239 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 239 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 366 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO B 367 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.024 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 261 2.73 - 3.27: 4305 3.27 - 3.82: 6575 3.82 - 4.36: 7277 4.36 - 4.90: 12570 Nonbonded interactions: 30988 Sorted by model distance: nonbonded pdb=" O PRO B 161 " pdb=" N LEU B 163 " model vdw 2.188 2.520 nonbonded pdb=" O VAL B 455 " pdb=" OG1 THR B 459 " model vdw 2.237 2.440 nonbonded pdb=" NH2 ARG A 183 " pdb=" O ILE B 490 " model vdw 2.241 2.520 nonbonded pdb=" O TRP A 179 " pdb=" OG1 THR A 182 " model vdw 2.248 2.440 nonbonded pdb=" O ILE B 378 " pdb=" OG SER B 382 " model vdw 2.250 2.440 ... (remaining 30983 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2631 2.51 5 N 625 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.400 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 0.043 4045 Z= 0.206 Angle : 0.678 7.320 5511 Z= 0.350 Chirality : 0.043 0.150 659 Planarity : 0.004 0.042 666 Dihedral : 14.105 80.165 1423 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.83 % Favored : 92.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.41), residues: 498 helix: 1.76 (0.30), residues: 346 sheet: None (None), residues: 0 loop : -1.99 (0.53), residues: 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1119 time to fit residues: 17.7628 Evaluate side-chains 96 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4045 Z= 0.196 Angle : 0.658 9.057 5511 Z= 0.330 Chirality : 0.042 0.133 659 Planarity : 0.004 0.028 666 Dihedral : 4.907 45.510 540 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer Outliers : 2.34 % 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: 0.88 (0.41), residues: 498 helix: 1.67 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.41 (0.54), residues: 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.478 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1033 time to fit residues: 14.5338 Evaluate side-chains 100 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0889 time to fit residues: 1.6359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4045 Z= 0.194 Angle : 0.632 6.930 5511 Z= 0.318 Chirality : 0.042 0.138 659 Planarity : 0.004 0.028 666 Dihedral : 4.893 46.656 540 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer Outliers : 1.40 % 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: 0.84 (0.40), residues: 498 helix: 1.67 (0.29), residues: 356 sheet: None (None), residues: 0 loop : -2.46 (0.52), residues: 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.476 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.1225 time to fit residues: 16.8099 Evaluate side-chains 93 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0460 time to fit residues: 1.0453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4045 Z= 0.186 Angle : 0.629 8.652 5511 Z= 0.314 Chirality : 0.042 0.146 659 Planarity : 0.004 0.028 666 Dihedral : 4.877 47.145 540 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer Outliers : 0.93 % 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: 0.82 (0.40), residues: 498 helix: 1.66 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.472 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.1196 time to fit residues: 16.4389 Evaluate side-chains 93 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0385 time to fit residues: 0.8145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4045 Z= 0.192 Angle : 0.636 7.342 5511 Z= 0.319 Chirality : 0.042 0.151 659 Planarity : 0.004 0.029 666 Dihedral : 4.878 47.389 540 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer Outliers : 1.64 % 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: 0.68 (0.40), residues: 498 helix: 1.59 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.66 (0.50), residues: 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.461 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.1154 time to fit residues: 15.5199 Evaluate side-chains 94 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0517 time to fit residues: 0.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4045 Z= 0.194 Angle : 0.668 13.086 5511 Z= 0.324 Chirality : 0.042 0.154 659 Planarity : 0.004 0.030 666 Dihedral : 4.888 47.367 540 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer Outliers : 1.87 % 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: 0.67 (0.40), residues: 498 helix: 1.55 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -2.72 (0.50), residues: 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.420 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.1107 time to fit residues: 15.0736 Evaluate side-chains 98 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0451 time to fit residues: 0.9558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4045 Z= 0.204 Angle : 0.688 13.755 5511 Z= 0.332 Chirality : 0.043 0.151 659 Planarity : 0.004 0.029 666 Dihedral : 4.926 47.560 540 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.43 % Favored : 93.17 % Rotamer Outliers : 2.10 % 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: 0.53 (0.40), residues: 498 helix: 1.50 (0.29), residues: 359 sheet: None (None), residues: 0 loop : -2.87 (0.49), residues: 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.491 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 0.1266 time to fit residues: 16.7520 Evaluate side-chains 95 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0481 time to fit residues: 0.8785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 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: 0.7575 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4045 Z= 0.200 Angle : 0.694 14.221 5511 Z= 0.336 Chirality : 0.043 0.154 659 Planarity : 0.004 0.031 666 Dihedral : 4.927 47.256 540 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer Outliers : 0.93 % 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: 0.53 (0.40), residues: 498 helix: 1.48 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -2.85 (0.49), residues: 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.468 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.1234 time to fit residues: 16.0005 Evaluate side-chains 96 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0502 time to fit residues: 0.7800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4045 Z= 0.202 Angle : 0.701 13.583 5511 Z= 0.342 Chirality : 0.044 0.179 659 Planarity : 0.004 0.031 666 Dihedral : 4.936 47.707 540 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer Outliers : 1.17 % 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 (0.40), residues: 498 helix: 1.39 (0.29), residues: 363 sheet: None (None), residues: 0 loop : -2.87 (0.50), residues: 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.1137 time to fit residues: 15.0159 Evaluate side-chains 98 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0463 time to fit residues: 0.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 4045 Z= 0.181 Angle : 0.716 14.844 5511 Z= 0.346 Chirality : 0.043 0.174 659 Planarity : 0.004 0.032 666 Dihedral : 5.049 49.923 540 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer Outliers : 0.47 % 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: 0.45 (0.40), residues: 498 helix: 1.28 (0.29), residues: 368 sheet: None (None), residues: 0 loop : -2.64 (0.52), residues: 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.466 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1217 time to fit residues: 17.2810 Evaluate side-chains 98 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0499 time to fit residues: 0.7006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.140911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129808 restraints weight = 8293.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132835 restraints weight = 4554.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134833 restraints weight = 2813.121| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 4045 Z= 0.202 Angle : 0.728 14.611 5511 Z= 0.352 Chirality : 0.044 0.162 659 Planarity : 0.004 0.030 666 Dihedral : 5.130 52.344 540 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.43 % Favored : 93.17 % Rotamer Outliers : 1.40 % 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: 0.31 (0.40), residues: 498 helix: 1.15 (0.29), residues: 370 sheet: None (None), residues: 0 loop : -2.63 (0.51), residues: 128 =============================================================================== Job complete usr+sys time: 1126.44 seconds wall clock time: 21 minutes 15.02 seconds (1275.02 seconds total)