Starting phenix.real_space_refine on Tue Aug 4 13:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wl_68052/08_2026/21wl_68052.map" } resolution = 3.7 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= 0.002 sd= 0.101 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 12 5.16 5 C 2231 2.51 5 N 561 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3491 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3491 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 11, 'TRANS': 440} Time building chain proxies: 1.06, per 1000 atoms: 0.30 Number of scatterers: 3491 At special positions: 0 Unit cell: (121.8, 100.8, 72.8, 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 12 16.00 O 687 8.00 N 561 7.00 C 2231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.29 Conformation dependent library (CDL) restraints added in 138.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 36.7% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'G' and resid 47 through 54 removed outlier: 3.665A pdb=" N LEU G 51 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 70 Processing helix chain 'G' and resid 122 through 134 Processing helix chain 'G' and resid 139 through 143 Processing helix chain 'G' and resid 179 through 191 removed outlier: 3.786A pdb=" N TYR G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 217 removed outlier: 3.639A pdb=" N GLY G 212 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 231 Processing helix chain 'G' and resid 237 through 244 Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 264 through 273 removed outlier: 4.058A pdb=" N VAL G 268 " --> pdb=" O PRO G 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE G 272 " --> pdb=" O VAL G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.652A pdb=" N GLN G 306 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 359 removed outlier: 3.995A pdb=" N VAL G 334 " --> pdb=" O TYR G 330 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 335 " --> pdb=" O VAL G 331 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE G 352 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 388 removed outlier: 4.080A pdb=" N THR G 377 " --> pdb=" O ARG G 373 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) Proline residue: G 380 - end of helix Processing helix chain 'G' and resid 420 through 426 removed outlier: 3.561A pdb=" N ASN G 424 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 42 through 44 removed outlier: 8.087A pdb=" N GLY G 81 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE G 30 " --> pdb=" O GLY G 81 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE G 222 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR G 221 " --> pdb=" O CYS G 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 144 through 149 removed outlier: 8.494A pdb=" N SER G 86 " --> pdb=" O PRO G 157 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU G 175 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR G 88 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS G 173 " --> pdb=" O THR G 88 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 90 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR G 171 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 110 through 116 Processing sheet with id=AA4, first strand: chain 'G' and resid 310 through 312 removed outlier: 3.917A pdb=" N ILE G 310 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 393 through 396 Processing sheet with id=AA6, first strand: chain 'G' and resid 409 through 411 133 hydrogen bonds defined for protein. 369 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: 0.45 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 661 1.33 - 1.45: 883 1.45 - 1.57: 1992 1.57 - 1.69: 1 1.69 - 1.81: 22 Bond restraints: 3559 Sorted by residual: bond pdb=" N ASN G 379 " pdb=" CA ASN G 379 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" N ASN G 135 " pdb=" CA ASN G 135 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.22e+01 bond pdb=" N VAL G 146 " pdb=" CA VAL G 146 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N VAL G 444 " pdb=" CA VAL G 444 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N VAL G 138 " pdb=" CA VAL G 138 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.19e-02 7.06e+03 1.06e+01 ... (remaining 3554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4423 1.25 - 2.50: 329 2.50 - 3.75: 70 3.75 - 4.99: 15 4.99 - 6.24: 6 Bond angle restraints: 4843 Sorted by residual: angle pdb=" CA ASP G 149 " pdb=" CB ASP G 149 " pdb=" CG ASP G 149 " ideal model delta sigma weight residual 112.60 116.41 -3.81 1.00e+00 1.00e+00 1.45e+01 angle pdb=" CA THR G 452 " pdb=" CB THR G 452 " pdb=" OG1 THR G 452 " ideal model delta sigma weight residual 109.60 103.91 5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA LEU G 451 " pdb=" C LEU G 451 " pdb=" O LEU G 451 " ideal model delta sigma weight residual 121.56 117.07 4.49 1.21e+00 6.83e-01 1.38e+01 angle pdb=" N SER G 366 " pdb=" CA SER G 366 " pdb=" C SER G 366 " ideal model delta sigma weight residual 114.75 110.22 4.53 1.26e+00 6.30e-01 1.29e+01 angle pdb=" CA VAL G 446 " pdb=" C VAL G 446 " pdb=" O VAL G 446 " ideal model delta sigma weight residual 121.64 118.12 3.52 9.80e-01 1.04e+00 1.29e+01 ... (remaining 4838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1895 16.25 - 32.51: 151 32.51 - 48.76: 37 48.76 - 65.01: 3 65.01 - 81.26: 5 Dihedral angle restraints: 2091 sinusoidal: 781 harmonic: 1310 Sorted by residual: dihedral pdb=" CA MET G 245 " pdb=" C MET G 245 " pdb=" N GLY G 246 " pdb=" CA GLY G 246 " ideal model delta harmonic sigma weight residual 180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO G 92 " pdb=" C PRO G 92 " pdb=" N VAL G 93 " pdb=" CA VAL G 93 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU G 314 " pdb=" C GLU G 314 " pdb=" N HIS G 315 " pdb=" CA HIS G 315 " ideal model delta harmonic sigma weight residual -180.00 -164.47 -15.53 0 5.00e+00 4.00e-02 9.65e+00 ... (remaining 2088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 413 0.047 - 0.095: 103 0.095 - 0.142: 38 0.142 - 0.189: 12 0.189 - 0.237: 5 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA PRO G 277 " pdb=" N PRO G 277 " pdb=" C PRO G 277 " pdb=" CB PRO G 277 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE G 372 " pdb=" N ILE G 372 " pdb=" C ILE G 372 " pdb=" CB ILE G 372 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR G 37 " pdb=" CA THR G 37 " pdb=" OG1 THR G 37 " pdb=" CG2 THR G 37 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 568 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 276 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO G 277 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO G 277 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 277 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 454 " -0.205 9.50e-02 1.11e+02 9.18e-02 5.19e+00 pdb=" NE ARG G 454 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 454 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 454 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 454 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 91 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO G 92 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 92 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 92 " 0.030 5.00e-02 4.00e+02 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1119 2.83 - 3.35: 2979 3.35 - 3.86: 4983 3.86 - 4.38: 5129 4.38 - 4.90: 9527 Nonbonded interactions: 23737 Sorted by model distance: nonbonded pdb=" O THR G 45 " pdb=" OG SER G 46 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR G 32 " pdb=" OD2 ASP G 200 " model vdw 2.359 3.040 nonbonded pdb=" N LEU G 451 " pdb=" CD2 LEU G 451 " model vdw 2.455 3.540 nonbonded pdb=" OE2 GLU G 204 " pdb=" NE2 GLN G 227 " model vdw 2.472 3.120 nonbonded pdb=" OG SER G 224 " pdb=" OE1 GLU G 265 " model vdw 2.483 3.040 ... (remaining 23732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.710 Find NCS groups from input model: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.006 0.075 3559 Z= 0.386 Angle : 0.770 6.242 4843 Z= 0.517 Chirality : 0.055 0.237 571 Planarity : 0.007 0.107 618 Dihedral : 13.114 81.262 1251 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.22 % Favored : 90.89 % Rotamer: Outliers : 0.52 % Allowed : 0.79 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.36), residues: 450 helix: 0.84 (0.43), residues: 135 sheet: -0.27 (0.52), residues: 99 loop : -2.33 (0.33), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 454 TYR 0.015 0.002 TYR G 333 PHE 0.010 0.001 PHE G 324 TRP 0.012 0.002 TRP G 196 HIS 0.003 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.39 ( 3559) covalent geometry : angle 0.77009 / 0.52 ( 4843) hydrogen bonds : bond 0.21887 / 15.05 ( 133) hydrogen bonds : angle 6.62420 / 4.52 ( 369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: G 113 PHE cc_start: 0.8305 (m-80) cc_final: 0.8083 (m-10) REVERT: G 140 TYR cc_start: 0.6507 (m-80) cc_final: 0.6272 (m-80) REVERT: G 245 MET cc_start: 0.8571 (ptp) cc_final: 0.7343 (tpt) REVERT: G 435 TYR cc_start: 0.8486 (p90) cc_final: 0.8151 (p90) outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.0472 time to fit residues: 6.9754 Evaluate side-chains 58 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 377 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097247 restraints weight = 7823.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099846 restraints weight = 3757.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101510 restraints weight = 2192.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102640 restraints weight = 1443.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103369 restraints weight = 1042.477| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3559 Z= 0.213 Angle : 0.683 6.464 4843 Z= 0.375 Chirality : 0.046 0.236 571 Planarity : 0.006 0.103 618 Dihedral : 5.174 44.074 482 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.44 % Favored : 91.11 % Rotamer: Outliers : 4.46 % Allowed : 10.50 % Favored : 85.04 % 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 are not related in a simple way. whole: -1.35 (0.36), residues: 450 helix: 0.60 (0.40), residues: 139 sheet: -0.40 (0.51), residues: 99 loop : -2.24 (0.34), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 241 TYR 0.017 0.002 TYR G 311 PHE 0.013 0.002 PHE G 69 TRP 0.011 0.002 TRP G 196 HIS 0.015 0.002 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 3559) covalent geometry : angle 0.68261 / 0.38 ( 4843) hydrogen bonds : bond 0.06369 / 4.17 ( 133) hydrogen bonds : angle 5.06901 / 3.57 ( 369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.136 Fit side-chains REVERT: G 95 GLU cc_start: 0.8282 (tt0) cc_final: 0.7921 (tm-30) REVERT: G 140 TYR cc_start: 0.7361 (m-80) cc_final: 0.6468 (m-80) REVERT: G 144 PHE cc_start: 0.7942 (m-80) cc_final: 0.7551 (m-80) REVERT: G 245 MET cc_start: 0.8956 (ptp) cc_final: 0.6856 (tpt) REVERT: G 300 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8187 (mt-10) REVERT: G 346 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: G 377 THR cc_start: 0.6522 (OUTLIER) cc_final: 0.6266 (p) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.0452 time to fit residues: 4.1842 Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096170 restraints weight = 8113.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098728 restraints weight = 3884.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100400 restraints weight = 2262.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101519 restraints weight = 1485.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102233 restraints weight = 1062.932| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3559 Z= 0.181 Angle : 0.605 6.651 4843 Z= 0.336 Chirality : 0.045 0.235 571 Planarity : 0.005 0.094 618 Dihedral : 5.048 38.623 482 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.44 % Favored : 91.11 % Rotamer: Outliers : 6.30 % Allowed : 11.81 % Favored : 81.89 % 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 are not related in a simple way. whole: -1.24 (0.36), residues: 450 helix: 0.80 (0.40), residues: 145 sheet: -0.61 (0.50), residues: 99 loop : -2.18 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 241 TYR 0.014 0.001 TYR G 311 PHE 0.009 0.001 PHE G 55 TRP 0.007 0.002 TRP G 255 HIS 0.003 0.001 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 3559) covalent geometry : angle 0.60494 / 0.34 ( 4843) hydrogen bonds : bond 0.05875 / 3.84 ( 133) hydrogen bonds : angle 4.73266 / 3.23 ( 369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: G 140 TYR cc_start: 0.7573 (m-80) cc_final: 0.6630 (m-80) REVERT: G 245 MET cc_start: 0.8990 (ptp) cc_final: 0.7010 (tpt) REVERT: G 300 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8521 (mt-10) REVERT: G 346 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7265 (mp0) outliers start: 24 outliers final: 17 residues processed: 69 average time/residue: 0.0473 time to fit residues: 4.4345 Evaluate side-chains 62 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096033 restraints weight = 7970.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098582 restraints weight = 3814.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100238 restraints weight = 2222.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101354 restraints weight = 1460.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101993 restraints weight = 1044.193| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3559 Z= 0.161 Angle : 0.581 6.684 4843 Z= 0.323 Chirality : 0.044 0.229 571 Planarity : 0.005 0.085 618 Dihedral : 4.649 16.960 481 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.22 % Favored : 91.33 % Rotamer: Outliers : 4.46 % Allowed : 14.96 % Favored : 80.58 % 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 are not related in a simple way. whole: -1.15 (0.36), residues: 450 helix: 1.02 (0.41), residues: 145 sheet: -0.71 (0.47), residues: 99 loop : -2.16 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 241 TYR 0.013 0.001 TYR G 311 PHE 0.007 0.001 PHE G 55 TRP 0.007 0.001 TRP G 255 HIS 0.002 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 3559) covalent geometry : angle 0.58091 / 0.32 ( 4843) hydrogen bonds : bond 0.05393 / 3.52 ( 133) hydrogen bonds : angle 4.54294 / 3.11 ( 369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: G 140 TYR cc_start: 0.7655 (m-80) cc_final: 0.6686 (m-80) REVERT: G 245 MET cc_start: 0.8960 (ptp) cc_final: 0.6970 (tpt) REVERT: G 300 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8585 (mt-10) REVERT: G 346 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: G 431 MET cc_start: 0.8425 (ptm) cc_final: 0.8182 (ptp) outliers start: 17 outliers final: 13 residues processed: 61 average time/residue: 0.0491 time to fit residues: 4.0489 Evaluate side-chains 57 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092711 restraints weight = 8226.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095100 restraints weight = 3957.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096675 restraints weight = 2316.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097741 restraints weight = 1528.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098346 restraints weight = 1095.781| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3559 Z= 0.236 Angle : 0.660 6.618 4843 Z= 0.366 Chirality : 0.048 0.454 571 Planarity : 0.005 0.079 618 Dihedral : 5.004 16.656 481 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.44 % Favored : 89.11 % Rotamer: Outliers : 6.82 % Allowed : 12.86 % Favored : 80.31 % 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 are not related in a simple way. whole: -1.33 (0.36), residues: 450 helix: 0.81 (0.41), residues: 147 sheet: -0.79 (0.48), residues: 97 loop : -2.24 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 426 TYR 0.015 0.002 TYR G 311 PHE 0.010 0.001 PHE G 55 TRP 0.010 0.002 TRP G 339 HIS 0.003 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 ( 3559) covalent geometry : angle 0.66013 / 0.37 ( 4843) hydrogen bonds : bond 0.06441 / 4.16 ( 133) hydrogen bonds : angle 4.79374 / 3.29 ( 369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: G 245 MET cc_start: 0.9062 (ptp) cc_final: 0.7173 (tpt) REVERT: G 325 MET cc_start: 0.8999 (mmm) cc_final: 0.8609 (mmp) REVERT: G 346 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: G 373 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8198 (tpt-90) outliers start: 26 outliers final: 20 residues processed: 63 average time/residue: 0.0520 time to fit residues: 4.3175 Evaluate side-chains 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 373 ARG Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098143 restraints weight = 8022.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100620 restraints weight = 3868.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102226 restraints weight = 2254.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103316 restraints weight = 1487.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104015 restraints weight = 1066.015| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3559 Z= 0.121 Angle : 0.561 6.674 4843 Z= 0.311 Chirality : 0.045 0.361 571 Planarity : 0.004 0.066 618 Dihedral : 4.505 18.134 481 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.56 % Favored : 92.00 % Rotamer: Outliers : 4.20 % Allowed : 16.54 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.36), residues: 450 helix: 1.18 (0.41), residues: 146 sheet: -0.63 (0.48), residues: 97 loop : -2.20 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 241 TYR 0.010 0.001 TYR G 333 PHE 0.004 0.001 PHE G 55 TRP 0.005 0.001 TRP G 255 HIS 0.001 0.000 HIS G 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3559) covalent geometry : angle 0.56075 / 0.31 ( 4843) hydrogen bonds : bond 0.04547 / 2.98 ( 133) hydrogen bonds : angle 4.34660 / 2.97 ( 369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.134 Fit side-chains REVERT: G 140 TYR cc_start: 0.7758 (m-80) cc_final: 0.6756 (m-80) REVERT: G 235 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: G 245 MET cc_start: 0.8874 (ptp) cc_final: 0.6852 (tpt) REVERT: G 325 MET cc_start: 0.8949 (mmm) cc_final: 0.8538 (mmp) REVERT: G 346 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7481 (mp0) outliers start: 16 outliers final: 12 residues processed: 59 average time/residue: 0.0480 time to fit residues: 3.8607 Evaluate side-chains 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 235 GLU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.0070 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101653 restraints weight = 8031.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104223 restraints weight = 3837.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105890 restraints weight = 2232.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107009 restraints weight = 1460.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107719 restraints weight = 1044.688| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 3559 Z= 0.108 Angle : 0.538 6.610 4843 Z= 0.295 Chirality : 0.044 0.344 571 Planarity : 0.004 0.056 618 Dihedral : 4.244 19.198 481 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.33 % Favored : 92.22 % Rotamer: Outliers : 3.67 % Allowed : 18.11 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.37), residues: 450 helix: 1.45 (0.42), residues: 146 sheet: -0.43 (0.48), residues: 99 loop : -2.05 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 241 TYR 0.008 0.001 TYR G 100 PHE 0.004 0.001 PHE G 44 TRP 0.004 0.001 TRP G 255 HIS 0.001 0.000 HIS G 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 3559) covalent geometry : angle 0.53832 / 0.30 ( 4843) hydrogen bonds : bond 0.03479 / 2.31 ( 133) hydrogen bonds : angle 4.08457 / 2.78 ( 369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.138 Fit side-chains REVERT: G 140 TYR cc_start: 0.7729 (m-80) cc_final: 0.6678 (m-80) REVERT: G 235 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: G 245 MET cc_start: 0.8676 (ptp) cc_final: 0.6788 (tpt) REVERT: G 325 MET cc_start: 0.8767 (mmm) cc_final: 0.8399 (mmp) REVERT: G 346 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 373 ARG cc_start: 0.8770 (tpt-90) cc_final: 0.8397 (ttt-90) REVERT: G 418 MET cc_start: 0.8453 (mtp) cc_final: 0.8164 (mtp) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.0608 time to fit residues: 4.8587 Evaluate side-chains 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 235 GLU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096446 restraints weight = 8161.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099040 restraints weight = 3891.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100677 restraints weight = 2251.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101825 restraints weight = 1470.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102537 restraints weight = 1041.937| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3559 Z= 0.132 Angle : 0.573 8.842 4843 Z= 0.310 Chirality : 0.043 0.321 571 Planarity : 0.003 0.048 618 Dihedral : 4.411 17.513 481 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.78 % Favored : 92.00 % Rotamer: Outliers : 4.20 % Allowed : 18.11 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.37), residues: 450 helix: 1.44 (0.42), residues: 146 sheet: -0.29 (0.49), residues: 99 loop : -1.99 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 83 TYR 0.011 0.001 TYR G 311 PHE 0.005 0.001 PHE G 55 TRP 0.006 0.001 TRP G 339 HIS 0.001 0.000 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3559) covalent geometry : angle 0.57276 / 0.31 ( 4843) hydrogen bonds : bond 0.04447 / 2.92 ( 133) hydrogen bonds : angle 4.17012 / 2.83 ( 369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.134 Fit side-chains REVERT: G 52 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8448 (pp30) REVERT: G 140 TYR cc_start: 0.7755 (m-80) cc_final: 0.6743 (m-80) REVERT: G 235 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: G 245 MET cc_start: 0.8830 (ptp) cc_final: 0.6805 (tpt) REVERT: G 325 MET cc_start: 0.8892 (mmm) cc_final: 0.8465 (mmp) REVERT: G 346 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: G 357 MET cc_start: 0.8024 (mmm) cc_final: 0.7287 (mmm) outliers start: 16 outliers final: 14 residues processed: 57 average time/residue: 0.0507 time to fit residues: 3.8937 Evaluate side-chains 57 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 235 GLU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 451 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101354 restraints weight = 7844.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103952 restraints weight = 3749.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105670 restraints weight = 2171.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106744 restraints weight = 1408.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107495 restraints weight = 1007.778| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3559 Z= 0.109 Angle : 0.554 7.895 4843 Z= 0.297 Chirality : 0.043 0.309 571 Planarity : 0.003 0.046 618 Dihedral : 4.182 19.867 481 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.33 % Favored : 92.44 % Rotamer: Outliers : 2.62 % Allowed : 20.73 % Favored : 76.64 % 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 are not related in a simple way. whole: -0.47 (0.38), residues: 450 helix: 1.65 (0.43), residues: 144 sheet: 0.05 (0.51), residues: 99 loop : -2.01 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 241 TYR 0.007 0.001 TYR G 311 PHE 0.004 0.001 PHE G 352 TRP 0.003 0.001 TRP G 194 HIS 0.001 0.000 HIS G 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 3559) covalent geometry : angle 0.55440 / 0.30 ( 4843) hydrogen bonds : bond 0.03257 / 2.18 ( 133) hydrogen bonds : angle 4.00111 / 2.71 ( 369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.133 Fit side-chains REVERT: G 44 PHE cc_start: 0.8677 (m-80) cc_final: 0.8424 (m-10) REVERT: G 52 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8477 (pp30) REVERT: G 140 TYR cc_start: 0.7737 (m-80) cc_final: 0.6642 (m-80) REVERT: G 245 MET cc_start: 0.8664 (ptp) cc_final: 0.6733 (tpt) REVERT: G 252 MET cc_start: 0.8611 (tmm) cc_final: 0.8068 (tmm) REVERT: G 325 MET cc_start: 0.8685 (mmm) cc_final: 0.8331 (mmp) REVERT: G 346 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: G 357 MET cc_start: 0.7740 (mmm) cc_final: 0.7472 (tpp) REVERT: G 373 ARG cc_start: 0.8758 (tpt-90) cc_final: 0.8449 (ttt90) REVERT: G 418 MET cc_start: 0.8501 (mtp) cc_final: 0.8121 (mtp) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.0551 time to fit residues: 4.0669 Evaluate side-chains 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097459 restraints weight = 8190.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100044 restraints weight = 3894.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101736 restraints weight = 2258.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102848 restraints weight = 1476.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103565 restraints weight = 1050.346| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3559 Z= 0.123 Angle : 0.570 7.492 4843 Z= 0.308 Chirality : 0.043 0.293 571 Planarity : 0.004 0.050 618 Dihedral : 4.205 17.956 481 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.00 % Favored : 91.78 % Rotamer: Outliers : 3.15 % Allowed : 20.21 % Favored : 76.64 % 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 are not related in a simple way. whole: -0.44 (0.38), residues: 450 helix: 1.54 (0.42), residues: 145 sheet: 0.10 (0.52), residues: 99 loop : -1.92 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 83 TYR 0.024 0.001 TYR G 100 PHE 0.004 0.001 PHE G 55 TRP 0.005 0.001 TRP G 339 HIS 0.001 0.000 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 3559) covalent geometry : angle 0.56958 / 0.31 ( 4843) hydrogen bonds : bond 0.04177 / 2.73 ( 133) hydrogen bonds : angle 4.05915 / 2.73 ( 369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.141 Fit side-chains REVERT: G 52 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8437 (pp30) REVERT: G 140 TYR cc_start: 0.7715 (m-80) cc_final: 0.6670 (m-80) REVERT: G 245 MET cc_start: 0.8786 (ptp) cc_final: 0.6988 (tpt) REVERT: G 322 ASP cc_start: 0.7053 (m-30) cc_final: 0.6659 (m-30) REVERT: G 325 MET cc_start: 0.8835 (mmm) cc_final: 0.8471 (mmp) REVERT: G 346 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: G 357 MET cc_start: 0.8008 (mmm) cc_final: 0.7763 (tpp) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.0502 time to fit residues: 3.6083 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095470 restraints weight = 8124.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097966 restraints weight = 3880.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099543 restraints weight = 2242.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100631 restraints weight = 1469.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101323 restraints weight = 1045.350| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3559 Z= 0.166 Angle : 0.618 7.211 4843 Z= 0.335 Chirality : 0.044 0.294 571 Planarity : 0.004 0.050 618 Dihedral : 4.538 17.357 481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 3.41 % Allowed : 20.73 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.37), residues: 450 helix: 1.30 (0.42), residues: 145 sheet: -0.01 (0.51), residues: 97 loop : -2.03 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 83 TYR 0.023 0.002 TYR G 100 PHE 0.007 0.001 PHE G 55 TRP 0.006 0.001 TRP G 339 HIS 0.002 0.001 HIS G 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3559) covalent geometry : angle 0.61778 / 0.33 ( 4843) hydrogen bonds : bond 0.05246 / 3.40 ( 133) hydrogen bonds : angle 4.34550 / 2.93 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 783.24 seconds wall clock time: 14 minutes 7.76 seconds (847.76 seconds total)