Starting phenix.real_space_refine on Wed Sep 17 05:36:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywe_39630/09_2025/8ywe_39630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywe_39630/09_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_39630/09_2025/8ywe_39630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywe_39630/09_2025/8ywe_39630.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywe_39630/09_2025/8ywe_39630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywe_39630/09_2025/8ywe_39630.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.45, per 1000 atoms: 0.28 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: 0.43 Conformation dependent library (CDL) restraints added in 223.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.19 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: 0.85 Time building geometry restraints manager: 0.62 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: 10.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- 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 : 4.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 143 TYR 0.007 0.001 TYR C 220 PHE 0.005 0.001 PHE A 497 TRP 0.010 0.001 TRP B 98 HIS 0.002 0.000 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5410) covalent geometry : angle 0.50213 ( 7348) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.51230 ( 16) hydrogen bonds : bond 0.23099 ( 174) hydrogen bonds : angle 9.64908 ( 480) *********************** 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 : 0.167 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: 0.7797 time to fit residues: 57.2051 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 : 0.181 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.2513 r_free = 0.2513 target = 0.035267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.032562 restraints weight = 20314.657| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 1.75 r_work: 0.2338 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2257 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9272 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5418 Z= 0.228 Angle : 0.621 6.617 7364 Z= 0.327 Chirality : 0.045 0.138 774 Planarity : 0.005 0.054 953 Dihedral : 5.352 58.703 758 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.83 % Allowed : 8.66 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.32), residues: 671 helix: -3.47 (0.57), residues: 41 sheet: 0.67 (0.32), residues: 254 loop : -0.74 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.016 0.002 TYR C 220 PHE 0.012 0.002 PHE A 377 TRP 0.010 0.001 TRP B 98 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 5410) covalent geometry : angle 0.62025 ( 7348) SS BOND : bond 0.00509 ( 8) SS BOND : angle 0.84498 ( 16) hydrogen bonds : bond 0.03928 ( 174) hydrogen bonds : angle 6.73574 ( 480) *********************** 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: 16 poor density : 41 time to evaluate : 0.204 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 53 average time/residue: 0.7669 time to fit residues: 42.0501 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS 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 34 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.0030 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.2968 ------------------------------------------------------------------------------- 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 = 0.2520 r_free = 0.2520 target = 0.035512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.032812 restraints weight = 20214.863| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 1.75 r_work: 0.2347 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9266 moved from start: 0.2046 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= 0.156 Angle : 0.548 6.140 7364 Z= 0.288 Chirality : 0.043 0.132 774 Planarity : 0.004 0.043 953 Dihedral : 4.730 28.487 756 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.83 % Allowed : 10.07 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.32), residues: 671 helix: -3.35 (0.55), residues: 41 sheet: 0.94 (0.33), residues: 252 loop : -0.43 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.012 0.001 TYR C 220 PHE 0.009 0.001 PHE A 377 TRP 0.010 0.001 TRP C 94 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5410) covalent geometry : angle 0.54770 ( 7348) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.69287 ( 16) hydrogen bonds : bond 0.03267 ( 174) hydrogen bonds : angle 6.30414 ( 480) *********************** 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 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.230 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 52 average time/residue: 0.7674 time to fit residues: 41.3558 Evaluate side-chains 44 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 258 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 19 optimal weight: 0.4980 chunk 54 optimal weight: 0.0970 overall best weight: 0.2196 ------------------------------------------------------------------------------- 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 = 0.2536 r_free = 0.2536 target = 0.035939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.033222 restraints weight = 20049.124| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 1.75 r_work: 0.2363 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2284 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9257 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5418 Z= 0.127 Angle : 0.525 5.899 7364 Z= 0.274 Chirality : 0.043 0.135 774 Planarity : 0.004 0.038 953 Dihedral : 4.586 28.644 756 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 11.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.32), residues: 671 helix: -3.24 (0.56), residues: 42 sheet: 0.99 (0.33), residues: 252 loop : -0.25 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.010 0.001 TYR B 219 PHE 0.016 0.001 PHE C 83 TRP 0.008 0.001 TRP C 94 HIS 0.003 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5410) covalent geometry : angle 0.52515 ( 7348) SS BOND : bond 0.00230 ( 8) SS BOND : angle 0.59352 ( 16) hydrogen bonds : bond 0.02862 ( 174) hydrogen bonds : angle 5.98712 ( 480) *********************** 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 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.205 Fit side-chains REVERT: C 228 ARG cc_start: 0.9486 (OUTLIER) cc_final: 0.7522 (mtm180) outliers start: 16 outliers final: 6 residues processed: 50 average time/residue: 0.7450 time to fit residues: 38.6234 Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 201 LYS 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 61 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.035212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.032494 restraints weight = 20534.134| |-----------------------------------------------------------------------------| r_work (start): 0.2413 rms_B_bonded: 1.76 r_work: 0.2336 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5418 Z= 0.165 Angle : 0.558 6.205 7364 Z= 0.290 Chirality : 0.043 0.128 774 Planarity : 0.004 0.045 953 Dihedral : 4.774 28.126 756 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 12.01 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.32), residues: 671 helix: -3.23 (0.56), residues: 42 sheet: 1.01 (0.33), residues: 253 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.011 0.001 TYR C 220 PHE 0.014 0.001 PHE C 83 TRP 0.008 0.001 TRP B 171 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5410) covalent geometry : angle 0.55786 ( 7348) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.62596 ( 16) hydrogen bonds : bond 0.02949 ( 174) hydrogen bonds : angle 6.01930 ( 480) *********************** 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 50 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.217 Fit side-chains REVERT: C 228 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.7543 (mtm180) outliers start: 14 outliers final: 6 residues processed: 47 average time/residue: 0.7212 time to fit residues: 35.2509 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 201 LYS 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 27 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.2480 r_free = 0.2480 target = 0.034319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.031650 restraints weight = 20608.647| |-----------------------------------------------------------------------------| r_work (start): 0.2383 rms_B_bonded: 1.75 r_work: 0.2304 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5418 Z= 0.213 Angle : 0.594 6.354 7364 Z= 0.311 Chirality : 0.044 0.128 774 Planarity : 0.004 0.050 953 Dihedral : 5.046 27.921 756 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.83 % Allowed : 12.01 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.32), residues: 671 helix: -3.24 (0.56), residues: 42 sheet: 1.04 (0.33), residues: 253 loop : -0.26 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.012 0.002 TYR C 220 PHE 0.014 0.002 PHE C 83 TRP 0.012 0.002 TRP C 94 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 5410) covalent geometry : angle 0.59394 ( 7348) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.71235 ( 16) hydrogen bonds : bond 0.03164 ( 174) hydrogen bonds : angle 6.17763 ( 480) *********************** 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 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.207 Fit side-chains REVERT: C 104 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8473 (mtpp) REVERT: C 228 ARG cc_start: 0.9513 (OUTLIER) cc_final: 0.7633 (mtm180) outliers start: 16 outliers final: 8 residues processed: 51 average time/residue: 0.7293 time to fit residues: 38.5710 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 : 0.229 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.2445 r_free = 0.2445 target = 0.033371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.030725 restraints weight = 20593.622| |-----------------------------------------------------------------------------| r_work (start): 0.2347 rms_B_bonded: 1.73 r_work: 0.2269 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2189 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9315 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5418 Z= 0.273 Angle : 0.648 6.656 7364 Z= 0.339 Chirality : 0.046 0.138 774 Planarity : 0.005 0.056 953 Dihedral : 5.343 27.588 756 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.83 % Allowed : 12.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.32), residues: 671 helix: -3.26 (0.55), residues: 42 sheet: 1.10 (0.33), residues: 253 loop : -0.36 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.013 0.002 TYR C 220 PHE 0.015 0.002 PHE C 83 TRP 0.013 0.002 TRP B 171 HIS 0.006 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 5410) covalent geometry : angle 0.64753 ( 7348) SS BOND : bond 0.00410 ( 8) SS BOND : angle 0.83702 ( 16) hydrogen bonds : bond 0.03434 ( 174) hydrogen bonds : angle 6.38843 ( 480) *********************** 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 51 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.214 Fit side-chains REVERT: C 94 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7574 (t-100) REVERT: C 104 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8489 (mtpp) REVERT: C 228 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.7691 (mtm180) outliers start: 16 outliers final: 8 residues processed: 48 average time/residue: 0.7081 time to fit residues: 35.2861 Evaluate side-chains 46 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 94 TRP 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 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 24 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 52 optimal weight: 0.0970 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.2497 r_free = 0.2497 target = 0.034839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.032165 restraints weight = 20131.166| |-----------------------------------------------------------------------------| r_work (start): 0.2401 rms_B_bonded: 1.74 r_work: 0.2323 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2243 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5418 Z= 0.151 Angle : 0.555 6.050 7364 Z= 0.290 Chirality : 0.043 0.147 774 Planarity : 0.004 0.041 953 Dihedral : 4.874 27.443 756 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.30 % Allowed : 12.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.33), residues: 671 helix: -3.25 (0.55), residues: 42 sheet: 1.11 (0.33), residues: 253 loop : -0.23 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.011 0.001 TYR B 219 PHE 0.017 0.001 PHE C 83 TRP 0.014 0.001 TRP C 94 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5410) covalent geometry : angle 0.55462 ( 7348) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.65161 ( 16) hydrogen bonds : bond 0.02897 ( 174) hydrogen bonds : angle 6.00798 ( 480) *********************** 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 48 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.260 Fit side-chains REVERT: C 228 ARG cc_start: 0.9508 (OUTLIER) cc_final: 0.7627 (mtm180) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 0.7668 time to fit residues: 36.6497 Evaluate side-chains 42 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 201 LYS 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 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.2479 r_free = 0.2479 target = 0.034331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.031659 restraints weight = 20572.091| |-----------------------------------------------------------------------------| r_work (start): 0.2382 rms_B_bonded: 1.75 r_work: 0.2304 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9293 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5418 Z= 0.188 Angle : 0.580 6.279 7364 Z= 0.304 Chirality : 0.044 0.150 774 Planarity : 0.004 0.046 953 Dihedral : 4.996 27.513 756 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.65 % Allowed : 12.90 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.33), residues: 671 helix: -3.24 (0.56), residues: 42 sheet: 1.14 (0.33), residues: 253 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.011 0.001 TYR B 219 PHE 0.021 0.002 PHE C 83 TRP 0.010 0.001 TRP B 171 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 5410) covalent geometry : angle 0.57986 ( 7348) SS BOND : bond 0.00302 ( 8) SS BOND : angle 0.68763 ( 16) hydrogen bonds : bond 0.03038 ( 174) hydrogen bonds : angle 6.06304 ( 480) *********************** 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 51 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.220 Fit side-chains REVERT: C 104 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8473 (mtpp) REVERT: C 228 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.7641 (mtm180) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 0.7033 time to fit residues: 35.0944 Evaluate side-chains 45 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.2489 r_free = 0.2489 target = 0.034622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.031947 restraints weight = 20576.722| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 1.76 r_work: 0.2314 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2234 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9288 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5418 Z= 0.172 Angle : 0.570 6.135 7364 Z= 0.299 Chirality : 0.044 0.146 774 Planarity : 0.004 0.043 953 Dihedral : 4.923 27.578 756 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.94 % Allowed : 13.78 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.33), residues: 671 helix: -3.24 (0.56), residues: 42 sheet: 1.13 (0.33), residues: 253 loop : -0.22 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.011 0.001 TYR C 220 PHE 0.009 0.001 PHE C 152 TRP 0.013 0.001 TRP C 94 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5410) covalent geometry : angle 0.56997 ( 7348) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.64967 ( 16) hydrogen bonds : bond 0.02940 ( 174) hydrogen bonds : angle 5.98304 ( 480) ********************** 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 47 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.211 Fit side-chains REVERT: C 104 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8472 (mtpp) REVERT: C 228 ARG cc_start: 0.9510 (OUTLIER) cc_final: 0.7574 (mtm180) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.7214 time to fit residues: 33.7517 Evaluate side-chains 46 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 214 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.2436 r_free = 0.2436 target = 0.033094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.030451 restraints weight = 20804.330| |-----------------------------------------------------------------------------| r_work (start): 0.2337 rms_B_bonded: 1.74 r_work: 0.2258 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9320 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 5418 Z= 0.297 Angle : 0.672 6.682 7364 Z= 0.352 Chirality : 0.047 0.162 774 Planarity : 0.005 0.061 953 Dihedral : 5.447 27.944 756 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.12 % Allowed : 13.78 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.33), residues: 671 helix: -3.27 (0.55), residues: 42 sheet: 1.13 (0.33), residues: 253 loop : -0.37 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.013 0.002 TYR C 220 PHE 0.019 0.002 PHE C 83 TRP 0.014 0.002 TRP B 171 HIS 0.006 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 5410) covalent geometry : angle 0.67113 ( 7348) SS BOND : bond 0.00430 ( 8) SS BOND : angle 0.89805 ( 16) hydrogen bonds : bond 0.03505 ( 174) hydrogen bonds : angle 6.37032 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.31 seconds wall clock time: 37 minutes 53.64 seconds (2273.64 seconds total)