Starting phenix.real_space_refine on Sat May 10 06:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywe_39630/05_2025/8ywe_39630.cif" } resolution = 2.69 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= -0.033 sd= 0.121 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 22 5.16 5 C 3337 2.51 5 N 893 2.21 5 O 1019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5271 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1599 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Time building chain proxies: 5.16, per 1000 atoms: 0.98 Number of scatterers: 5271 At special positions: 0 Unit cell: (89.25, 91.63, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1019 8.00 N 893 7.00 C 3337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 221 " 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 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 673.4 milliseconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 15 sheets defined 9.5% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.634A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.181A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.678A pdb=" N GLU B 84 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.758A pdb=" N HIS B 156 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.689A pdb=" N GLY C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.550A pdb=" N THR C 216 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.880A pdb=" N LEU C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.570A pdb=" N PHE C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 359 removed outlier: 3.808A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.521A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.696A pdb=" N ASN B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 131 Processing sheet with id=AA8, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AA9, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.617A pdb=" N TRP B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 174 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.617A pdb=" N TRP B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 174 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.702A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.900A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.533A pdb=" N SER C 144 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 135 removed outlier: 4.139A pdb=" N ALA C 156 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET C 157 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE C 173 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP C 159 " --> pdb=" O VAL C 171 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 480 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: 1.76 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 853 1.28 - 1.42: 1501 1.42 - 1.55: 3027 1.55 - 1.68: 1 1.68 - 1.81: 28 Bond restraints: 5410 Sorted by residual: bond pdb=" C GLN C 27 " pdb=" O GLN C 27 " ideal model delta sigma weight residual 1.234 1.152 0.082 1.31e-02 5.83e+03 3.95e+01 bond pdb=" CA GLN C 27 " pdb=" C GLN C 27 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.24e-02 6.50e+03 2.38e+01 bond pdb=" CA GLN C 27 " pdb=" CB GLN C 27 " ideal model delta sigma weight residual 1.534 1.457 0.078 1.60e-02 3.91e+03 2.35e+01 bond pdb=" N GLN C 27 " pdb=" CA GLN C 27 " ideal model delta sigma weight residual 1.454 1.427 0.027 1.31e-02 5.83e+03 4.40e+00 bond pdb=" CA TYR C 32 " pdb=" C TYR C 32 " ideal model delta sigma weight residual 1.523 1.503 0.021 1.34e-02 5.57e+03 2.35e+00 ... (remaining 5405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7256 1.73 - 3.46: 76 3.46 - 5.20: 12 5.20 - 6.93: 2 6.93 - 8.66: 2 Bond angle restraints: 7348 Sorted by residual: angle pdb=" N SER C 28 " pdb=" CA SER C 28 " pdb=" C SER C 28 " ideal model delta sigma weight residual 109.15 117.81 -8.66 1.44e+00 4.82e-01 3.62e+01 angle pdb=" N GLN C 27 " pdb=" CA GLN C 27 " pdb=" CB GLN C 27 " ideal model delta sigma weight residual 111.05 104.69 6.36 1.50e+00 4.44e-01 1.79e+01 angle pdb=" CA GLN C 27 " pdb=" C GLN C 27 " pdb=" O GLN C 27 " ideal model delta sigma weight residual 121.68 117.12 4.56 1.18e+00 7.18e-01 1.50e+01 angle pdb=" N TYR C 32 " pdb=" CA TYR C 32 " pdb=" C TYR C 32 " ideal model delta sigma weight residual 110.80 103.48 7.32 2.13e+00 2.20e-01 1.18e+01 angle pdb=" N VAL C 29 " pdb=" CA VAL C 29 " pdb=" C VAL C 29 " ideal model delta sigma weight residual 109.34 102.78 6.56 2.08e+00 2.31e-01 9.94e+00 ... (remaining 7343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3026 16.42 - 32.83: 125 32.83 - 49.25: 16 49.25 - 65.66: 5 65.66 - 82.08: 1 Dihedral angle restraints: 3173 sinusoidal: 1225 harmonic: 1948 Sorted by residual: dihedral pdb=" N GLN C 27 " pdb=" C GLN C 27 " pdb=" CA GLN C 27 " pdb=" CB GLN C 27 " ideal model delta harmonic sigma weight residual 122.80 111.14 11.66 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C GLN C 27 " pdb=" N GLN C 27 " pdb=" CA GLN C 27 " pdb=" CB GLN C 27 " ideal model delta harmonic sigma weight residual -122.60 -111.63 -10.97 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 123.76 -30.76 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 3170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 607 0.044 - 0.089: 115 0.089 - 0.133: 47 0.133 - 0.177: 1 0.177 - 0.222: 4 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA SER C 28 " pdb=" N SER C 28 " pdb=" C SER C 28 " pdb=" CB SER C 28 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA SER C 31 " pdb=" N SER C 31 " pdb=" C SER C 31 " pdb=" CB SER C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL C 29 " pdb=" N VAL C 29 " pdb=" C VAL C 29 " pdb=" CB VAL C 29 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 771 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 463 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 521 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 44 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B 45 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " 0.014 5.00e-02 4.00e+02 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1668 2.83 - 3.34: 4289 3.34 - 3.86: 8631 3.86 - 4.38: 10354 4.38 - 4.90: 17912 Nonbonded interactions: 42854 Sorted by model distance: nonbonded pdb=" N VAL B 34 " pdb=" OD1 ASN B 52 " model vdw 2.308 3.120 nonbonded pdb=" O TYR C 155 " pdb=" NH2 ARG C 197 " model vdw 2.312 3.120 nonbonded pdb=" NH2 ARG C 192 " pdb=" OD2 ASP C 215 " model vdw 2.366 3.120 nonbonded pdb=" OG1 THR B 33 " pdb=" OD1 ASN B 52 " model vdw 2.378 3.040 nonbonded pdb=" NE2 GLN C 38 " pdb=" OE1 GLN C 162 " model vdw 2.389 3.120 ... (remaining 42849 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=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: 7.520 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 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 0.082 5418 Z= 0.165 Angle : 0.502 8.659 7364 Z= 0.283 Chirality : 0.043 0.222 774 Planarity : 0.003 0.027 953 Dihedral : 9.063 82.080 1921 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.77 % Allowed : 5.12 % Favored : 93.11 % Cbeta Deviations : 0.16 % 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: -1.47 (0.31), residues: 671 helix: -4.09 (0.40), residues: 40 sheet: -0.01 (0.32), residues: 255 loop : -1.32 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 98 HIS 0.002 0.000 HIS B 159 PHE 0.005 0.001 PHE A 497 TYR 0.007 0.001 TYR C 220 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.23099 ( 174) hydrogen bonds : angle 9.64908 ( 480) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.51230 ( 16) covalent geometry : bond 0.00266 ( 5410) covalent geometry : angle 0.50213 ( 7348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.555 Fit side-chains REVERT: C 224 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8974 (m-30) outliers start: 10 outliers final: 1 residues processed: 71 average time/residue: 1.4952 time to fit residues: 109.9933 Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 224 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 16 GLN B 32 ASN B 35 ASN B 38 GLN B 97 ASN B 127 GLN B 243 GLN C 27 GLN C 37 GLN C 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.035639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.032925 restraints weight = 20091.966| |-----------------------------------------------------------------------------| r_work (start): 0.2429 rms_B_bonded: 1.75 r_work: 0.2351 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2270 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5418 Z= 0.210 Angle : 0.605 6.518 7364 Z= 0.319 Chirality : 0.044 0.135 774 Planarity : 0.005 0.051 953 Dihedral : 5.274 59.476 758 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.65 % Allowed : 8.66 % Favored : 88.69 % 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: -0.55 (0.32), residues: 671 helix: -3.46 (0.57), residues: 41 sheet: 0.68 (0.32), residues: 254 loop : -0.73 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 171 HIS 0.004 0.001 HIS B 159 PHE 0.012 0.002 PHE A 377 TYR 0.015 0.002 TYR C 220 ARG 0.004 0.001 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 174) hydrogen bonds : angle 6.67733 ( 480) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.79808 ( 16) covalent geometry : bond 0.00491 ( 5410) covalent geometry : angle 0.60461 ( 7348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.618 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 1.5497 time to fit residues: 85.3364 Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.0000 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.035012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.032329 restraints weight = 20179.986| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 1.73 r_work: 0.2330 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2251 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5418 Z= 0.184 Angle : 0.571 6.310 7364 Z= 0.300 Chirality : 0.044 0.143 774 Planarity : 0.004 0.046 953 Dihedral : 4.854 28.191 756 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.36 % Allowed : 9.72 % Favored : 86.93 % 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: -0.22 (0.32), residues: 671 helix: -3.39 (0.55), residues: 41 sheet: 0.92 (0.33), residues: 253 loop : -0.49 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 171 HIS 0.004 0.001 HIS B 159 PHE 0.009 0.002 PHE A 377 TYR 0.013 0.001 TYR C 220 ARG 0.003 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 174) hydrogen bonds : angle 6.40297 ( 480) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.73293 ( 16) covalent geometry : bond 0.00435 ( 5410) covalent geometry : angle 0.57051 ( 7348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.609 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 53 average time/residue: 1.4805 time to fit residues: 81.7186 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 0.0170 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.2504 r_free = 0.2504 target = 0.034998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.032287 restraints weight = 20735.658| |-----------------------------------------------------------------------------| r_work (start): 0.2407 rms_B_bonded: 1.76 r_work: 0.2329 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5418 Z= 0.166 Angle : 0.560 6.176 7364 Z= 0.293 Chirality : 0.043 0.133 774 Planarity : 0.004 0.043 953 Dihedral : 4.832 28.183 756 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.18 % Allowed : 10.78 % Favored : 86.04 % 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: -0.06 (0.32), residues: 671 helix: -3.30 (0.55), residues: 42 sheet: 0.97 (0.33), residues: 253 loop : -0.32 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 94 HIS 0.004 0.001 HIS B 159 PHE 0.016 0.001 PHE C 83 TYR 0.011 0.001 TYR C 220 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 174) hydrogen bonds : angle 6.15273 ( 480) SS BOND : bond 0.00288 ( 8) SS BOND : angle 0.66030 ( 16) covalent geometry : bond 0.00392 ( 5410) covalent geometry : angle 0.55999 ( 7348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.598 Fit side-chains REVERT: C 228 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.7603 (mtm180) outliers start: 18 outliers final: 5 residues processed: 52 average time/residue: 1.4354 time to fit residues: 77.9905 Evaluate side-chains 42 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 47 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.035141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.032456 restraints weight = 20137.093| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 1.74 r_work: 0.2335 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5418 Z= 0.156 Angle : 0.552 6.110 7364 Z= 0.288 Chirality : 0.043 0.146 774 Planarity : 0.004 0.045 953 Dihedral : 4.777 27.783 756 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.83 % Allowed : 11.31 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 671 helix: -3.29 (0.55), residues: 42 sheet: 1.04 (0.33), residues: 253 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.004 0.001 HIS A 445 PHE 0.014 0.001 PHE C 83 TYR 0.011 0.001 TYR B 219 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 174) hydrogen bonds : angle 6.00493 ( 480) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.64261 ( 16) covalent geometry : bond 0.00369 ( 5410) covalent geometry : angle 0.55173 ( 7348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.613 Fit side-chains REVERT: C 104 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: C 228 ARG cc_start: 0.9501 (OUTLIER) cc_final: 0.7556 (mtm180) outliers start: 16 outliers final: 7 residues processed: 48 average time/residue: 1.6366 time to fit residues: 81.6123 Evaluate side-chains 44 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.033944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.031290 restraints weight = 20388.443| |-----------------------------------------------------------------------------| r_work (start): 0.2368 rms_B_bonded: 1.73 r_work: 0.2290 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5418 Z= 0.230 Angle : 0.609 6.451 7364 Z= 0.319 Chirality : 0.045 0.144 774 Planarity : 0.005 0.051 953 Dihedral : 5.131 27.983 756 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.47 % Allowed : 12.19 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.32), residues: 671 helix: -3.29 (0.54), residues: 42 sheet: 1.05 (0.33), residues: 253 loop : -0.30 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.005 0.001 HIS B 159 PHE 0.014 0.002 PHE C 83 TYR 0.012 0.002 TYR C 220 ARG 0.004 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 174) hydrogen bonds : angle 6.21853 ( 480) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.75746 ( 16) covalent geometry : bond 0.00547 ( 5410) covalent geometry : angle 0.60884 ( 7348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.843 Fit side-chains REVERT: C 104 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: C 228 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.7654 (mtm180) outliers start: 14 outliers final: 7 residues processed: 47 average time/residue: 1.4235 time to fit residues: 69.8373 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 38 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.034458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.031801 restraints weight = 20015.386| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 1.73 r_work: 0.2310 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2230 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9289 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5418 Z= 0.183 Angle : 0.578 8.152 7364 Z= 0.301 Chirality : 0.044 0.130 774 Planarity : 0.004 0.046 953 Dihedral : 4.979 27.481 756 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.30 % Allowed : 12.72 % Favored : 84.98 % 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: 0.11 (0.33), residues: 671 helix: -3.25 (0.56), residues: 42 sheet: 1.15 (0.33), residues: 253 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 94 HIS 0.004 0.001 HIS A 445 PHE 0.016 0.002 PHE C 83 TYR 0.011 0.001 TYR B 219 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 174) hydrogen bonds : angle 6.06691 ( 480) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.66197 ( 16) covalent geometry : bond 0.00435 ( 5410) covalent geometry : angle 0.57782 ( 7348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.637 Fit side-chains REVERT: C 104 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8466 (mtpp) REVERT: C 228 ARG cc_start: 0.9510 (OUTLIER) cc_final: 0.7635 (mtm180) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 1.4420 time to fit residues: 67.7387 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.034211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.031554 restraints weight = 20338.801| |-----------------------------------------------------------------------------| r_work (start): 0.2378 rms_B_bonded: 1.74 r_work: 0.2299 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2219 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5418 Z= 0.197 Angle : 0.587 7.893 7364 Z= 0.307 Chirality : 0.044 0.129 774 Planarity : 0.004 0.045 953 Dihedral : 5.048 27.596 756 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.65 % Allowed : 12.37 % Favored : 84.98 % 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: 0.11 (0.33), residues: 671 helix: -3.26 (0.55), residues: 42 sheet: 1.16 (0.33), residues: 253 loop : -0.25 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.004 0.001 HIS A 445 PHE 0.020 0.002 PHE C 83 TYR 0.013 0.001 TYR B 219 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 174) hydrogen bonds : angle 6.08640 ( 480) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.68685 ( 16) covalent geometry : bond 0.00469 ( 5410) covalent geometry : angle 0.58634 ( 7348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.628 Fit side-chains REVERT: B 235 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: C 104 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8477 (mtpp) REVERT: C 228 ARG cc_start: 0.9513 (OUTLIER) cc_final: 0.7642 (mtm180) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 1.3732 time to fit residues: 68.8508 Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 65 optimal weight: 0.0970 chunk 10 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.036119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.033411 restraints weight = 20075.565| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 1.77 r_work: 0.2367 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5418 Z= 0.106 Angle : 0.522 7.549 7364 Z= 0.272 Chirality : 0.042 0.131 774 Planarity : 0.004 0.035 953 Dihedral : 4.530 27.270 756 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.98 % 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: 0.27 (0.33), residues: 671 helix: -3.22 (0.56), residues: 42 sheet: 1.21 (0.33), residues: 252 loop : -0.08 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 94 HIS 0.005 0.001 HIS A 445 PHE 0.020 0.001 PHE C 83 TYR 0.011 0.001 TYR B 219 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 174) hydrogen bonds : angle 5.65416 ( 480) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.55788 ( 16) covalent geometry : bond 0.00249 ( 5410) covalent geometry : angle 0.52223 ( 7348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.552 Fit side-chains REVERT: C 228 ARG cc_start: 0.9486 (OUTLIER) cc_final: 0.7546 (mtm180) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 1.5228 time to fit residues: 74.4263 Evaluate side-chains 41 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 0.0270 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 30 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.036181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.033461 restraints weight = 20318.631| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 1.78 r_work: 0.2369 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5418 Z= 0.112 Angle : 0.523 7.457 7364 Z= 0.273 Chirality : 0.042 0.131 774 Planarity : 0.004 0.034 953 Dihedral : 4.470 27.470 756 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.77 % Allowed : 13.25 % Favored : 84.98 % 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: 0.34 (0.33), residues: 671 helix: -3.19 (0.57), residues: 42 sheet: 1.25 (0.33), residues: 252 loop : -0.03 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 94 HIS 0.005 0.001 HIS A 445 PHE 0.022 0.001 PHE C 83 TYR 0.012 0.001 TYR B 219 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 174) hydrogen bonds : angle 5.56282 ( 480) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.57703 ( 16) covalent geometry : bond 0.00265 ( 5410) covalent geometry : angle 0.52295 ( 7348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.555 Fit side-chains REVERT: C 228 ARG cc_start: 0.9487 (OUTLIER) cc_final: 0.7544 (mtm180) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 1.4993 time to fit residues: 68.6161 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.0060 chunk 57 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.036568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.033844 restraints weight = 20359.148| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 1.78 r_work: 0.2382 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2301 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9245 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5418 Z= 0.106 Angle : 0.516 7.412 7364 Z= 0.269 Chirality : 0.042 0.128 774 Planarity : 0.004 0.033 953 Dihedral : 4.388 27.617 756 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 13.60 % Favored : 84.81 % 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: 0.39 (0.33), residues: 671 helix: -3.13 (0.59), residues: 41 sheet: 1.28 (0.33), residues: 252 loop : 0.01 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 94 HIS 0.004 0.001 HIS A 445 PHE 0.007 0.001 PHE C 152 TYR 0.012 0.001 TYR B 219 ARG 0.002 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 174) hydrogen bonds : angle 5.47413 ( 480) SS BOND : bond 0.00193 ( 8) SS BOND : angle 0.54028 ( 16) covalent geometry : bond 0.00252 ( 5410) covalent geometry : angle 0.51545 ( 7348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3811.23 seconds wall clock time: 66 minutes 43.68 seconds (4003.68 seconds total)