Starting phenix.real_space_refine on Thu Jun 5 05:34:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywe_39630/06_2025/8ywe_39630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywe_39630/06_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_39630/06_2025/8ywe_39630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywe_39630/06_2025/8ywe_39630.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywe_39630/06_2025/8ywe_39630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywe_39630/06_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.88, per 1000 atoms: 1.12 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: 1.30 Conformation dependent library (CDL) restraints added in 607.0 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: 0.78 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: 1.68 Time building geometry restraints manager: 1.57 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: 6.590 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.990 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- 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 : 0.558 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: 1.5284 time to fit residues: 112.4560 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 : 0.617 ------------------------------------------------------------------------------- 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 = 33)----------------| | 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 : 0.636 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 1.5246 time to fit residues: 84.0168 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 : 0.566 ------------------------------------------------------------------------------- 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: 0.2980 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.0060 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 overall best weight: 0.2802 ------------------------------------------------------------------------------- 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 = 0.2529 r_free = 0.2529 target = 0.035741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.033044 restraints weight = 20109.747| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 1.75 r_work: 0.2356 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9260 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5418 Z= 0.148 Angle : 0.541 6.091 7364 Z= 0.284 Chirality : 0.043 0.141 774 Planarity : 0.004 0.043 953 Dihedral : 4.665 28.638 756 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -0.15 (0.32), residues: 671 helix: -3.35 (0.55), residues: 41 sheet: 0.95 (0.33), residues: 252 loop : -0.41 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B 159 PHE 0.008 0.001 PHE A 377 TYR 0.011 0.001 TYR C 220 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 174) hydrogen bonds : angle 6.25211 ( 480) SS BOND : bond 0.00273 ( 8) SS BOND : angle 0.66666 ( 16) covalent geometry : bond 0.00346 ( 5410) covalent geometry : angle 0.54107 ( 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 59 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.612 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 54 average time/residue: 1.4517 time to fit residues: 81.6314 Evaluate side-chains 43 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.2452 r_free = 0.2452 target = 0.033542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.030890 restraints weight = 20920.297| |-----------------------------------------------------------------------------| r_work (start): 0.2355 rms_B_bonded: 1.75 r_work: 0.2276 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2197 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 5418 Z= 0.274 Angle : 0.644 6.608 7364 Z= 0.339 Chirality : 0.046 0.145 774 Planarity : 0.005 0.056 953 Dihedral : 5.271 28.200 756 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.36 % Allowed : 10.60 % 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: -0.14 (0.32), residues: 671 helix: -3.35 (0.55), residues: 41 sheet: 0.96 (0.33), residues: 253 loop : -0.43 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 171 HIS 0.007 0.001 HIS B 159 PHE 0.016 0.002 PHE C 83 TYR 0.014 0.002 TYR C 220 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 174) hydrogen bonds : angle 6.49867 ( 480) SS BOND : bond 0.00399 ( 8) SS BOND : angle 0.83843 ( 16) covalent geometry : bond 0.00651 ( 5410) covalent geometry : angle 0.64330 ( 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: 19 poor density : 37 time to evaluate : 0.587 Fit side-chains REVERT: C 94 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7902 (t-100) REVERT: C 104 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8495 (mtpp) REVERT: C 228 ARG cc_start: 0.9527 (OUTLIER) cc_final: 0.7678 (mtm180) outliers start: 19 outliers final: 8 residues processed: 51 average time/residue: 1.4508 time to fit residues: 77.0878 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 : 0.674 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 34 optimal weight: 0.0270 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.2490 r_free = 0.2490 target = 0.034676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.031998 restraints weight = 20182.983| |-----------------------------------------------------------------------------| r_work (start): 0.2395 rms_B_bonded: 1.73 r_work: 0.2317 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9285 moved from start: 0.2394 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= 0.162 Angle : 0.560 6.133 7364 Z= 0.293 Chirality : 0.043 0.135 774 Planarity : 0.004 0.044 953 Dihedral : 4.913 27.709 756 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.65 % Allowed : 11.84 % 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 (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 (0.33), residues: 671 helix: -3.30 (0.55), residues: 42 sheet: 1.04 (0.33), residues: 253 loop : -0.29 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 94 HIS 0.003 0.001 HIS B 159 PHE 0.013 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 0.03057 ( 174) hydrogen bonds : angle 6.12668 ( 480) SS BOND : bond 0.00282 ( 8) SS BOND : angle 0.67569 ( 16) covalent geometry : bond 0.00382 ( 5410) covalent geometry : angle 0.55973 ( 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: 15 poor density : 37 time to evaluate : 0.547 Fit side-chains REVERT: C 228 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.7619 (mtm180) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 1.5687 time to fit residues: 79.8514 Evaluate side-chains 44 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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 107 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 58 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.2475 r_free = 0.2475 target = 0.034242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.031596 restraints weight = 20378.310| |-----------------------------------------------------------------------------| r_work (start): 0.2379 rms_B_bonded: 1.74 r_work: 0.2301 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2221 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.2482 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= 0.190 Angle : 0.580 6.266 7364 Z= 0.304 Chirality : 0.044 0.134 774 Planarity : 0.004 0.047 953 Dihedral : 5.009 27.934 756 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.18 % Allowed : 11.48 % 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: 0.05 (0.33), residues: 671 helix: -3.27 (0.55), residues: 42 sheet: 1.10 (0.33), residues: 253 loop : -0.28 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 94 HIS 0.004 0.001 HIS B 159 PHE 0.015 0.002 PHE C 83 TYR 0.012 0.001 TYR B 219 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 174) hydrogen bonds : angle 6.13844 ( 480) SS BOND : bond 0.00298 ( 8) SS BOND : angle 0.69456 ( 16) covalent geometry : bond 0.00450 ( 5410) covalent geometry : angle 0.57937 ( 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 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.567 Fit side-chains REVERT: C 228 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.7636 (mtm180) outliers start: 18 outliers final: 9 residues processed: 50 average time/residue: 1.5883 time to fit residues: 82.6171 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 : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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 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 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.2460 r_free = 0.2460 target = 0.033815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.031169 restraints weight = 20146.934| |-----------------------------------------------------------------------------| r_work (start): 0.2363 rms_B_bonded: 1.71 r_work: 0.2286 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2206 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9304 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5418 Z= 0.222 Angle : 0.605 6.433 7364 Z= 0.317 Chirality : 0.045 0.132 774 Planarity : 0.005 0.051 953 Dihedral : 5.157 27.703 756 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.65 % Allowed : 12.01 % 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: 0.05 (0.33), residues: 671 helix: -3.27 (0.55), residues: 42 sheet: 1.13 (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 0.016 0.002 PHE C 83 TYR 0.012 0.002 TYR B 219 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 174) hydrogen bonds : angle 6.21461 ( 480) SS BOND : bond 0.00345 ( 8) SS BOND : angle 0.73669 ( 16) covalent geometry : bond 0.00528 ( 5410) covalent geometry : angle 0.60450 ( 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 51 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.557 Fit side-chains REVERT: C 94 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7626 (t-100) REVERT: C 104 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: C 228 ARG cc_start: 0.9519 (OUTLIER) cc_final: 0.7648 (mtm180) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 1.6197 time to fit residues: 80.8285 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.2423 r_free = 0.2423 target = 0.032760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.030136 restraints weight = 20602.813| |-----------------------------------------------------------------------------| r_work (start): 0.2324 rms_B_bonded: 1.72 r_work: 0.2247 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2167 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.2714 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= 0.314 Angle : 0.684 6.812 7364 Z= 0.358 Chirality : 0.047 0.148 774 Planarity : 0.005 0.064 953 Dihedral : 5.555 28.032 756 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.36 % Allowed : 11.66 % 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: -0.01 (0.33), residues: 671 helix: -3.30 (0.55), residues: 42 sheet: 1.15 (0.33), residues: 253 loop : -0.40 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 171 HIS 0.006 0.001 HIS B 159 PHE 0.019 0.002 PHE C 83 TYR 0.014 0.002 TYR C 220 ARG 0.006 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 174) hydrogen bonds : angle 6.46809 ( 480) SS BOND : bond 0.00459 ( 8) SS BOND : angle 0.93542 ( 16) covalent geometry : bond 0.00748 ( 5410) covalent geometry : angle 0.68297 ( 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 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.574 Fit side-chains REVERT: B 235 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: C 94 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7568 (t-100) REVERT: C 104 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8506 (mtpp) REVERT: C 228 ARG cc_start: 0.9535 (OUTLIER) cc_final: 0.7709 (mtm180) outliers start: 19 outliers final: 9 residues processed: 51 average time/residue: 1.3967 time to fit residues: 74.4661 Evaluate side-chains 49 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 99 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 46 optimal weight: 0.2980 chunk 65 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 = 0.2501 r_free = 0.2501 target = 0.035013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.032356 restraints weight = 20195.241| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 1.75 r_work: 0.2329 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2250 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5418 Z= 0.129 Angle : 0.548 7.620 7364 Z= 0.285 Chirality : 0.043 0.146 774 Planarity : 0.004 0.037 953 Dihedral : 4.831 27.155 756 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.65 % Allowed : 12.72 % Favored : 84.63 % 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: 0.10 (0.33), residues: 671 helix: -3.26 (0.56), residues: 42 sheet: 1.13 (0.33), residues: 253 loop : -0.25 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 94 HIS 0.002 0.001 HIS B 159 PHE 0.020 0.001 PHE C 83 TYR 0.012 0.001 TYR B 219 ARG 0.002 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 174) hydrogen bonds : angle 5.92356 ( 480) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.64116 ( 16) covalent geometry : bond 0.00305 ( 5410) covalent geometry : angle 0.54812 ( 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 50 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.611 Fit side-chains REVERT: B 235 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8794 (pt0) REVERT: C 228 ARG cc_start: 0.9501 (OUTLIER) cc_final: 0.7559 (mtm180) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 1.4088 time to fit residues: 70.6579 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 : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 THR 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 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: 0.8980 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 46 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 overall best weight: 0.2784 ------------------------------------------------------------------------------- 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 = 0.2494 r_free = 0.2494 target = 0.034815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.032145 restraints weight = 20411.948| |-----------------------------------------------------------------------------| r_work (start): 0.2397 rms_B_bonded: 1.75 r_work: 0.2321 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2242 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 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 0.051 5418 Z= 0.151 Angle : 0.560 8.089 7364 Z= 0.291 Chirality : 0.043 0.146 774 Planarity : 0.004 0.044 953 Dihedral : 4.837 27.367 756 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.94 % Allowed : 13.96 % 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 (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: 0.14 (0.33), residues: 671 helix: -3.23 (0.56), residues: 42 sheet: 1.17 (0.33), residues: 253 loop : -0.22 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 171 HIS 0.003 0.001 HIS B 159 PHE 0.009 0.001 PHE C 173 TYR 0.014 0.001 TYR B 219 ARG 0.003 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 174) hydrogen bonds : angle 5.89035 ( 480) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.64793 ( 16) covalent geometry : bond 0.00360 ( 5410) covalent geometry : angle 0.55991 ( 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 46 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.630 Fit side-chains REVERT: B 235 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (pt0) REVERT: C 228 ARG cc_start: 0.9507 (OUTLIER) cc_final: 0.7617 (mtm180) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 1.5383 time to fit residues: 72.1438 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 212 THR 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 134 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLU 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: 0.2980 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.0570 chunk 57 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 overall best weight: 0.2898 ------------------------------------------------------------------------------- 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 = 0.2495 r_free = 0.2495 target = 0.034846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.032175 restraints weight = 20484.267| |-----------------------------------------------------------------------------| r_work (start): 0.2398 rms_B_bonded: 1.75 r_work: 0.2323 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2243 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5418 Z= 0.154 Angle : 0.561 8.144 7364 Z= 0.292 Chirality : 0.043 0.145 774 Planarity : 0.004 0.041 953 Dihedral : 4.836 27.327 756 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.12 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 (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: 0.15 (0.33), residues: 671 helix: -3.24 (0.56), residues: 42 sheet: 1.17 (0.33), residues: 253 loop : -0.21 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 94 HIS 0.003 0.001 HIS B 159 PHE 0.018 0.001 PHE C 83 TYR 0.013 0.001 TYR B 219 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 174) hydrogen bonds : angle 5.87017 ( 480) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.63201 ( 16) covalent geometry : bond 0.00368 ( 5410) covalent geometry : angle 0.56055 ( 7348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4149.37 seconds wall clock time: 71 minutes 43.13 seconds (4303.13 seconds total)