Starting phenix.real_space_refine on Mon Mar 11 07:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0k_15786/03_2024/8b0k_15786.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3725 atoms to isotropic. 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 13 5.16 5 C 2519 2.51 5 N 635 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3830 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3830 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 33, 'TRANS': 458} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 2.53, per 1000 atoms: 0.66 Number of scatterers: 3830 At special positions: 0 Unit cell: (58.646, 84.252, 87.556, 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 13 16.00 O 663 8.00 N 635 7.00 C 2519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 951.8 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 55.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 25 through 28 removed outlier: 3.890A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.970A pdb=" N ALA A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 removed outlier: 3.863A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.522A pdb=" N THR A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.011A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.686A pdb=" N ALA A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.826A pdb=" N ILE A 156 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 removed outlier: 4.434A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.569A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 4.299A pdb=" N LEU A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.547A pdb=" N LEU A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.314A pdb=" N TRP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 removed outlier: 3.594A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 4.244A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 4.244A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.666A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 385 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 564 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: 1.46 Time building geometry restraints manager: 1.72 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: 1191 1.34 - 1.46: 820 1.46 - 1.57: 1904 1.57 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 3938 Sorted by residual: bond pdb=" C TRP A 489 " pdb=" N PRO A 490 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.29e-01 bond pdb=" N LEU A 208 " pdb=" CA LEU A 208 " ideal model delta sigma weight residual 1.462 1.454 0.008 1.31e-02 5.83e+03 4.17e-01 bond pdb=" CA TRP A 34 " pdb=" C TRP A 34 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.26e-02 6.30e+03 3.75e-01 bond pdb=" C GLN A 278 " pdb=" N PRO A 279 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.69e-01 bond pdb=" C TRP A 34 " pdb=" N PRO A 35 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.19e-02 7.06e+03 3.57e-01 ... (remaining 3933 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 162 106.85 - 113.63: 2140 113.63 - 120.42: 1477 120.42 - 127.20: 1541 127.20 - 133.98: 64 Bond angle restraints: 5384 Sorted by residual: angle pdb=" C LEU A 143 " pdb=" N THR A 144 " pdb=" CA THR A 144 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.03e+00 angle pdb=" N GLY A 69 " pdb=" CA GLY A 69 " pdb=" C GLY A 69 " ideal model delta sigma weight residual 115.66 111.53 4.13 1.56e+00 4.11e-01 7.02e+00 angle pdb=" N TRP A 489 " pdb=" CA TRP A 489 " pdb=" C TRP A 489 " ideal model delta sigma weight residual 109.81 114.63 -4.82 2.21e+00 2.05e-01 4.77e+00 angle pdb=" CA TRP A 489 " pdb=" C TRP A 489 " pdb=" N PRO A 490 " ideal model delta sigma weight residual 118.44 121.72 -3.28 1.59e+00 3.96e-01 4.25e+00 angle pdb=" N TRP A 34 " pdb=" CA TRP A 34 " pdb=" C TRP A 34 " ideal model delta sigma weight residual 109.81 113.83 -4.02 2.21e+00 2.05e-01 3.30e+00 ... (remaining 5379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 2150 13.82 - 27.64: 109 27.64 - 41.46: 26 41.46 - 55.27: 8 55.27 - 69.09: 1 Dihedral angle restraints: 2294 sinusoidal: 883 harmonic: 1411 Sorted by residual: dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual -180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA THR A 315 " pdb=" C THR A 315 " pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta harmonic sigma weight residual 180.00 165.06 14.94 0 5.00e+00 4.00e-02 8.93e+00 dihedral pdb=" N ARG A 11 " pdb=" CA ARG A 11 " pdb=" CB ARG A 11 " pdb=" CG ARG A 11 " ideal model delta sinusoidal sigma weight residual -180.00 -132.26 -47.74 3 1.50e+01 4.44e-03 8.54e+00 ... (remaining 2291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 353 0.028 - 0.056: 171 0.056 - 0.083: 38 0.083 - 0.111: 42 0.111 - 0.139: 9 Chirality restraints: 613 Sorted by residual: chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA TRP A 489 " pdb=" N TRP A 489 " pdb=" C TRP A 489 " pdb=" CB TRP A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE A 263 " pdb=" N ILE A 263 " pdb=" C ILE A 263 " pdb=" CB ILE A 263 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 610 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 422 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 205 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 35 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.017 5.00e-02 4.00e+02 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 981 2.80 - 3.33: 3746 3.33 - 3.85: 6569 3.85 - 4.38: 7901 4.38 - 4.90: 13618 Nonbonded interactions: 32815 Sorted by model distance: nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.276 2.440 nonbonded pdb=" O ASN A 334 " pdb=" NE2 GLN A 372 " model vdw 2.334 2.520 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.336 2.440 nonbonded pdb=" NE2 GLN A 228 " pdb=" O THR A 466 " model vdw 2.354 2.520 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.366 2.520 ... (remaining 32810 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.100 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.110 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.002 0.028 3938 Z= 0.158 Angle : 0.518 6.431 5384 Z= 0.256 Chirality : 0.042 0.139 613 Planarity : 0.005 0.068 676 Dihedral : 9.633 69.092 1390 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.50 % Allowed : 5.28 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.40), residues: 488 helix: 1.17 (0.34), residues: 245 sheet: -0.17 (0.60), residues: 68 loop : -0.42 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.008 0.001 PHE A 426 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.386 Fit side-chains REVERT: A 113 SER cc_start: 0.8170 (m) cc_final: 0.7934 (m) REVERT: A 380 ILE cc_start: 0.7992 (mp) cc_final: 0.7682 (mt) REVERT: A 488 ASN cc_start: 0.7928 (t0) cc_final: 0.7563 (t0) outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.8108 time to fit residues: 58.7938 Evaluate side-chains 53 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.0060 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 233 GLN A 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3938 Z= 0.171 Angle : 0.554 6.746 5384 Z= 0.275 Chirality : 0.042 0.144 613 Planarity : 0.005 0.062 676 Dihedral : 4.058 22.890 532 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.02 % Allowed : 9.05 % Favored : 87.94 % 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: 0.72 (0.40), residues: 488 helix: 1.24 (0.34), residues: 255 sheet: -0.05 (0.57), residues: 68 loop : -0.35 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.001 0.000 HIS A 425 PHE 0.017 0.001 PHE A 174 TYR 0.007 0.001 TYR A 388 ARG 0.002 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.463 Fit side-chains REVERT: A 113 SER cc_start: 0.8283 (m) cc_final: 0.8031 (m) REVERT: A 380 ILE cc_start: 0.8083 (mp) cc_final: 0.7779 (mt) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.6505 time to fit residues: 39.5105 Evaluate side-chains 53 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 244 ASN A 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3938 Z= 0.217 Angle : 0.566 9.309 5384 Z= 0.278 Chirality : 0.043 0.139 613 Planarity : 0.005 0.060 676 Dihedral : 4.009 19.527 531 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.52 % Allowed : 10.55 % Favored : 85.93 % 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: 0.60 (0.40), residues: 488 helix: 1.18 (0.34), residues: 255 sheet: -0.22 (0.56), residues: 68 loop : -0.44 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.000 0.000 HIS A 425 PHE 0.015 0.001 PHE A 174 TYR 0.007 0.001 TYR A 313 ARG 0.001 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8337 (m) cc_final: 0.8074 (m) REVERT: A 380 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7749 (mt) outliers start: 14 outliers final: 5 residues processed: 56 average time/residue: 0.6964 time to fit residues: 41.5199 Evaluate side-chains 52 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 244 ASN A 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3938 Z= 0.305 Angle : 0.612 9.611 5384 Z= 0.304 Chirality : 0.045 0.140 613 Planarity : 0.005 0.059 676 Dihedral : 4.349 23.877 531 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.02 % Allowed : 10.30 % Favored : 85.68 % 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: 0.35 (0.39), residues: 488 helix: 0.99 (0.33), residues: 255 sheet: -0.20 (0.59), residues: 60 loop : -0.63 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.000 0.000 HIS A 337 PHE 0.014 0.001 PHE A 174 TYR 0.009 0.001 TYR A 76 ARG 0.002 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.402 Fit side-chains REVERT: A 113 SER cc_start: 0.8453 (m) cc_final: 0.8174 (m) REVERT: A 311 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6880 (t0) REVERT: A 318 THR cc_start: 0.8657 (p) cc_final: 0.8457 (p) REVERT: A 380 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 16 outliers final: 8 residues processed: 64 average time/residue: 0.5984 time to fit residues: 40.9995 Evaluate side-chains 59 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3938 Z= 0.176 Angle : 0.559 9.552 5384 Z= 0.274 Chirality : 0.042 0.134 613 Planarity : 0.004 0.058 676 Dihedral : 4.072 19.635 531 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.27 % Allowed : 10.55 % Favored : 85.18 % 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: 0.64 (0.40), residues: 488 helix: 1.30 (0.34), residues: 248 sheet: -0.20 (0.57), residues: 68 loop : -0.49 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.000 0.000 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.013 0.001 TYR A 100 ARG 0.001 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.438 Fit side-chains REVERT: A 113 SER cc_start: 0.8293 (m) cc_final: 0.8020 (m) REVERT: A 380 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7819 (mt) outliers start: 17 outliers final: 8 residues processed: 55 average time/residue: 0.5893 time to fit residues: 34.7825 Evaluate side-chains 53 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.0020 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3938 Z= 0.159 Angle : 0.544 9.190 5384 Z= 0.264 Chirality : 0.042 0.139 613 Planarity : 0.004 0.057 676 Dihedral : 3.920 17.707 531 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.52 % Allowed : 11.31 % Favored : 85.18 % 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: 0.79 (0.40), residues: 488 helix: 1.45 (0.34), residues: 248 sheet: -0.14 (0.58), residues: 68 loop : -0.46 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.001 0.000 HIS A 425 PHE 0.019 0.001 PHE A 416 TYR 0.010 0.001 TYR A 100 ARG 0.001 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8300 (m) cc_final: 0.8023 (m) REVERT: A 380 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7817 (mt) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.6873 time to fit residues: 38.1277 Evaluate side-chains 54 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3938 Z= 0.173 Angle : 0.556 10.416 5384 Z= 0.269 Chirality : 0.042 0.138 613 Planarity : 0.004 0.057 676 Dihedral : 3.906 17.767 531 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.77 % Allowed : 11.31 % Favored : 84.92 % 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: 488 helix: 1.48 (0.34), residues: 248 sheet: -0.16 (0.58), residues: 68 loop : -0.45 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.001 0.000 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 100 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8299 (m) cc_final: 0.8015 (m) REVERT: A 380 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7817 (mt) outliers start: 15 outliers final: 9 residues processed: 54 average time/residue: 0.6615 time to fit residues: 38.0999 Evaluate side-chains 55 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0270 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3938 Z= 0.174 Angle : 0.557 10.243 5384 Z= 0.270 Chirality : 0.042 0.135 613 Planarity : 0.004 0.056 676 Dihedral : 3.894 17.733 531 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.02 % Allowed : 12.56 % Favored : 84.42 % 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: 0.83 (0.40), residues: 488 helix: 1.50 (0.34), residues: 248 sheet: -0.17 (0.57), residues: 68 loop : -0.46 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.019 0.001 PHE A 416 TYR 0.007 0.001 TYR A 100 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8302 (m) cc_final: 0.8018 (m) REVERT: A 380 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7806 (mt) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.6168 time to fit residues: 35.0272 Evaluate side-chains 55 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3938 Z= 0.177 Angle : 0.565 10.942 5384 Z= 0.271 Chirality : 0.042 0.136 613 Planarity : 0.004 0.056 676 Dihedral : 3.898 17.816 531 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.77 % Allowed : 12.06 % Favored : 84.17 % 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: 0.81 (0.40), residues: 488 helix: 1.49 (0.34), residues: 248 sheet: -0.18 (0.57), residues: 68 loop : -0.48 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.007 0.001 TYR A 100 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8319 (m) cc_final: 0.8031 (m) REVERT: A 318 THR cc_start: 0.8736 (p) cc_final: 0.8422 (p) REVERT: A 380 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7806 (mt) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.6199 time to fit residues: 33.8617 Evaluate side-chains 54 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3938 Z= 0.146 Angle : 0.552 10.168 5384 Z= 0.265 Chirality : 0.042 0.133 613 Planarity : 0.004 0.057 676 Dihedral : 3.786 16.099 531 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.51 % Allowed : 13.57 % Favored : 83.92 % 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: 0.93 (0.40), residues: 488 helix: 1.61 (0.34), residues: 248 sheet: -0.05 (0.58), residues: 67 loop : -0.50 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.017 0.001 PHE A 416 TYR 0.007 0.001 TYR A 100 ARG 0.001 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8283 (m) cc_final: 0.7992 (m) REVERT: A 380 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7800 (mt) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.7198 time to fit residues: 37.5481 Evaluate side-chains 51 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.119869 restraints weight = 4708.421| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.44 r_work: 0.3411 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3938 Z= 0.162 Angle : 0.560 10.967 5384 Z= 0.268 Chirality : 0.042 0.134 613 Planarity : 0.004 0.057 676 Dihedral : 3.800 16.651 531 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.26 % Allowed : 14.07 % Favored : 83.67 % 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: 0.92 (0.40), residues: 488 helix: 1.60 (0.34), residues: 248 sheet: -0.01 (0.58), residues: 67 loop : -0.51 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.007 0.001 TYR A 100 ARG 0.001 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.02 seconds wall clock time: 29 minutes 34.04 seconds (1774.04 seconds total)