Starting phenix.real_space_refine on Thu Nov 14 01:46:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/11_2024/9fgu_50428.cif" } resolution = 4.3 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= -0.004 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2071 2.51 5 N 545 2.21 5 O 612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1541 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 11, 'TRANS': 179} Chain: "E" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1686 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.63, per 1000 atoms: 1.12 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.01, 64.897, 92.456, 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 612 8.00 N 545 7.00 C 2071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 419.2 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.889A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.641A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.836A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.860A pdb=" N TYR E 79 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 97 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.509A pdb=" N CYS E 156 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 208 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.289A pdb=" N LEU E 144 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 219 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR E 170 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU E 167 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE E 182 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP E 169 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU E 180 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN E 171 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS E 173 " --> pdb=" O GLN E 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.289A pdb=" N LEU E 144 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 224 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR E 232 " --> pdb=" O GLU E 224 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.95 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: 1037 1.34 - 1.46: 864 1.46 - 1.58: 1409 1.58 - 1.70: 0 1.70 - 1.81: 15 Bond restraints: 3325 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.33e-02 5.65e+03 1.14e+00 bond pdb=" C3 NAG C1301 " pdb=" O3 NAG C1301 " ideal model delta sigma weight residual 1.403 1.422 -0.019 2.00e-02 2.50e+03 9.39e-01 ... (remaining 3320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4226 1.28 - 2.57: 231 2.57 - 3.85: 49 3.85 - 5.13: 8 5.13 - 6.42: 6 Bond angle restraints: 4520 Sorted by residual: angle pdb=" N GLY C 431 " pdb=" CA GLY C 431 " pdb=" C GLY C 431 " ideal model delta sigma weight residual 112.04 106.92 5.12 1.02e+00 9.61e-01 2.52e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" O GLY C 431 " ideal model delta sigma weight residual 122.45 118.86 3.59 7.20e-01 1.93e+00 2.49e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.38 114.61 -6.23 1.35e+00 5.49e-01 2.13e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" N CYS C 432 " ideal model delta sigma weight residual 114.29 119.03 -4.74 1.41e+00 5.03e-01 1.13e+01 angle pdb=" N ALA E 218 " pdb=" CA ALA E 218 " pdb=" C ALA E 218 " ideal model delta sigma weight residual 107.88 112.26 -4.38 1.41e+00 5.03e-01 9.64e+00 ... (remaining 4515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 1762 17.27 - 34.54: 162 34.54 - 51.81: 25 51.81 - 69.07: 9 69.07 - 86.34: 6 Dihedral angle restraints: 1964 sinusoidal: 773 harmonic: 1191 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -149.47 63.47 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -26.72 -59.28 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CA CYS C 379 " pdb=" C CYS C 379 " pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 299 0.033 - 0.066: 115 0.066 - 0.098: 43 0.098 - 0.131: 30 0.131 - 0.164: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" CG LEU E 85 " pdb=" CB LEU E 85 " pdb=" CD1 LEU E 85 " pdb=" CD2 LEU E 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ASP C 428 " pdb=" N ASP C 428 " pdb=" C ASP C 428 " pdb=" CB ASP C 428 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 485 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 479 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 108 " 0.008 2.00e-02 2.50e+03 9.29e-03 2.16e+00 pdb=" CG TRP E 108 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 108 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP E 108 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 108 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 108 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 108 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 192 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO E 193 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 193 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 193 " -0.016 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 87 2.68 - 3.23: 3289 3.23 - 3.79: 4956 3.79 - 4.34: 6344 4.34 - 4.90: 9980 Nonbonded interactions: 24656 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR E 90 " pdb=" O VAL E 114 " model vdw 2.202 3.040 nonbonded pdb=" O TRP C 353 " pdb=" NH2 ARG C 466 " model vdw 2.205 3.120 nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 43 " model vdw 2.252 3.120 nonbonded pdb=" NH1 ARG E 211 " pdb=" O LEU E 212 " model vdw 2.260 3.120 ... (remaining 24651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.730 Find NCS groups from input model: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 0.033 3325 Z= 0.216 Angle : 0.715 6.419 4520 Z= 0.407 Chirality : 0.045 0.164 488 Planarity : 0.004 0.047 585 Dihedral : 13.955 86.342 1195 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.40), residues: 407 helix: -1.17 (1.14), residues: 20 sheet: -0.09 (0.51), residues: 111 loop : -1.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 108 HIS 0.001 0.001 HIS C 519 PHE 0.019 0.002 PHE E 58 TYR 0.009 0.001 TYR C 365 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.339 Fit side-chains REVERT: E 238 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7604 (ttm110) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.2026 time to fit residues: 15.7625 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS E 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3325 Z= 0.190 Angle : 0.685 8.762 4520 Z= 0.351 Chirality : 0.047 0.164 488 Planarity : 0.004 0.039 585 Dihedral : 6.516 59.910 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % 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: -1.17 (0.41), residues: 407 helix: -0.57 (1.20), residues: 21 sheet: -0.15 (0.50), residues: 114 loop : -1.11 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.013 0.001 PHE C 392 TYR 0.014 0.001 TYR C 489 ARG 0.003 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 471 GLU cc_start: 0.6457 (pm20) cc_final: 0.6053 (pm20) REVERT: E 238 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7111 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2039 time to fit residues: 14.7117 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.167 Angle : 0.659 8.702 4520 Z= 0.332 Chirality : 0.046 0.161 488 Planarity : 0.004 0.034 585 Dihedral : 6.190 58.484 480 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % 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: -1.23 (0.41), residues: 407 helix: -1.25 (0.98), residues: 27 sheet: -0.20 (0.50), residues: 114 loop : -1.06 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.010 0.001 PHE E 217 TYR 0.011 0.001 TYR C 508 ARG 0.004 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.395 Fit side-chains REVERT: E 47 TRP cc_start: 0.8587 (t60) cc_final: 0.8345 (t60) REVERT: E 230 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.8096 (ptp-170) REVERT: E 238 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.7023 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2090 time to fit residues: 15.2706 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.0270 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.178 Angle : 0.642 7.226 4520 Z= 0.323 Chirality : 0.046 0.154 488 Planarity : 0.004 0.031 585 Dihedral : 6.088 58.554 480 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.41), residues: 407 helix: -1.48 (0.96), residues: 27 sheet: -0.19 (0.50), residues: 117 loop : -1.08 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 169 HIS 0.000 0.000 HIS C 505 PHE 0.016 0.001 PHE E 58 TYR 0.009 0.001 TYR C 508 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.9030 (tmm160) cc_final: 0.8757 (tmm160) REVERT: C 444 LYS cc_start: 0.6321 (ttpt) cc_final: 0.6046 (ttpt) REVERT: E 47 TRP cc_start: 0.8535 (t60) cc_final: 0.8329 (t60) REVERT: E 230 ARG cc_start: 0.8502 (ptp-170) cc_final: 0.8184 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2268 time to fit residues: 16.3141 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7198 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3325 Z= 0.223 Angle : 0.683 8.512 4520 Z= 0.343 Chirality : 0.046 0.170 488 Planarity : 0.004 0.031 585 Dihedral : 6.416 58.966 480 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % 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: -1.37 (0.41), residues: 407 helix: -1.38 (1.00), residues: 27 sheet: -0.38 (0.49), residues: 119 loop : -1.13 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.010 0.001 PHE E 233 TYR 0.009 0.001 TYR E 183 ARG 0.005 0.001 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.379 Fit side-chains REVERT: C 408 ARG cc_start: 0.9020 (tmm160) cc_final: 0.8761 (tmm160) REVERT: C 444 LYS cc_start: 0.6155 (ttpt) cc_final: 0.5913 (ttpt) REVERT: E 47 TRP cc_start: 0.8590 (t60) cc_final: 0.8379 (t60) REVERT: E 89 ASP cc_start: 0.4525 (p0) cc_final: 0.4267 (p0) REVERT: E 230 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8164 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2180 time to fit residues: 15.4012 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3325 Z= 0.177 Angle : 0.682 8.451 4520 Z= 0.340 Chirality : 0.046 0.153 488 Planarity : 0.004 0.035 585 Dihedral : 6.205 58.597 480 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -1.32 (0.41), residues: 407 helix: -1.39 (1.00), residues: 27 sheet: -0.47 (0.49), residues: 119 loop : -1.02 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.017 0.001 PHE E 58 TYR 0.006 0.001 TYR C 508 ARG 0.004 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.383 Fit side-chains REVERT: C 408 ARG cc_start: 0.9018 (tmm160) cc_final: 0.8720 (tmm160) REVERT: C 444 LYS cc_start: 0.6181 (ttpt) cc_final: 0.5925 (ttpt) REVERT: C 453 TYR cc_start: 0.7279 (p90) cc_final: 0.7018 (p90) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2040 time to fit residues: 14.0532 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3325 Z= 0.206 Angle : 0.689 7.621 4520 Z= 0.342 Chirality : 0.046 0.187 488 Planarity : 0.004 0.036 585 Dihedral : 6.283 58.490 480 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -1.40 (0.41), residues: 407 helix: -1.34 (1.02), residues: 27 sheet: -0.46 (0.49), residues: 116 loop : -1.12 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.019 0.001 PHE C 392 TYR 0.009 0.001 TYR C 449 ARG 0.004 0.001 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.383 Fit side-chains REVERT: C 408 ARG cc_start: 0.9033 (tmm160) cc_final: 0.8762 (tmm160) REVERT: C 444 LYS cc_start: 0.6200 (ttpt) cc_final: 0.5934 (ttpt) REVERT: C 453 TYR cc_start: 0.7299 (p90) cc_final: 0.7007 (p90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1914 time to fit residues: 12.8052 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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: 0.7144 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.174 Angle : 0.678 8.636 4520 Z= 0.334 Chirality : 0.046 0.208 488 Planarity : 0.004 0.039 585 Dihedral : 6.109 57.890 480 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -1.28 (0.42), residues: 407 helix: -1.24 (1.03), residues: 27 sheet: -0.42 (0.49), residues: 116 loop : -1.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 169 HIS 0.007 0.002 HIS C 505 PHE 0.016 0.001 PHE E 58 TYR 0.007 0.001 TYR E 220 ARG 0.003 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.323 Fit side-chains REVERT: C 408 ARG cc_start: 0.8999 (tmm160) cc_final: 0.8701 (tmm160) REVERT: C 444 LYS cc_start: 0.6263 (ttpt) cc_final: 0.6022 (ttpt) REVERT: C 453 TYR cc_start: 0.7321 (p90) cc_final: 0.7015 (p90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1869 time to fit residues: 13.1542 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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: 0.7116 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.162 Angle : 0.647 7.241 4520 Z= 0.323 Chirality : 0.046 0.183 488 Planarity : 0.004 0.038 585 Dihedral : 5.981 57.668 480 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.42), residues: 407 helix: 0.43 (1.55), residues: 15 sheet: -0.38 (0.49), residues: 118 loop : -0.94 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 169 HIS 0.008 0.003 HIS C 505 PHE 0.013 0.001 PHE C 392 TYR 0.008 0.001 TYR C 508 ARG 0.003 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.383 Fit side-chains REVERT: C 408 ARG cc_start: 0.8998 (tmm160) cc_final: 0.8679 (tmm160) REVERT: C 444 LYS cc_start: 0.6205 (ttpt) cc_final: 0.5992 (ttpt) REVERT: C 453 TYR cc_start: 0.7277 (p90) cc_final: 0.6943 (p90) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1901 time to fit residues: 13.0016 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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: 0.7133 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.178 Angle : 0.655 7.379 4520 Z= 0.327 Chirality : 0.046 0.174 488 Planarity : 0.004 0.037 585 Dihedral : 6.002 56.489 480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.27 (0.42), residues: 407 helix: -1.91 (0.95), residues: 26 sheet: -0.37 (0.49), residues: 118 loop : -0.95 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 169 HIS 0.000 0.000 HIS C 519 PHE 0.015 0.001 PHE E 58 TYR 0.007 0.001 TYR E 183 ARG 0.003 0.000 ARG E 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.9015 (tmm160) cc_final: 0.8694 (tmm160) REVERT: C 453 TYR cc_start: 0.7285 (p90) cc_final: 0.6933 (p90) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1943 time to fit residues: 13.3934 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.104714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093654 restraints weight = 12422.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095997 restraints weight = 7647.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097594 restraints weight = 5222.116| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3325 Z= 0.235 Angle : 0.696 8.150 4520 Z= 0.351 Chirality : 0.047 0.176 488 Planarity : 0.004 0.039 585 Dihedral : 6.398 58.243 480 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.48 (0.42), residues: 407 helix: -1.89 (0.97), residues: 27 sheet: -0.43 (0.50), residues: 115 loop : -1.16 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 169 HIS 0.022 0.007 HIS C 505 PHE 0.023 0.002 PHE C 392 TYR 0.010 0.001 TYR C 449 ARG 0.003 0.001 ARG E 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.32 seconds wall clock time: 25 minutes 43.30 seconds (1543.30 seconds total)