Starting phenix.real_space_refine on Fri Oct 23 00:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z5i_73816/10_2026/9z5i_73816.map" } resolution = 3.34 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= 0.000 sd= 0.045 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2358 2.51 5 N 538 2.21 5 O 610 1.98 5 H 3601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7120 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 7120 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Time building chain proxies: 1.49, per 1000 atoms: 0.21 Number of scatterers: 7120 At special positions: 0 Unit cell: (76.335, 71.246, 78.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 610 8.00 N 538 7.00 C 2358 6.00 H 3601 1.00 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: 0.71 Conformation dependent library (CDL) restraints added in 352.6 milliseconds 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 83.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 71 through 102 removed outlier: 3.921A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Proline residue: A 88 - end of helix Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.227A pdb=" N SER A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 140 through 159 Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 175 through 205 removed outlier: 4.017A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 4.880A pdb=" N GLY A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 256 through 279 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.576A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 removed outlier: 4.331A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.829A pdb=" N THR A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 352 through 368 Proline residue: A 360 - end of helix removed outlier: 3.660A pdb=" N TYR A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 397 removed outlier: 4.227A pdb=" N PHE A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 407 through 440 removed outlier: 3.804A pdb=" N VAL A 413 " --> pdb=" O TYR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 475 removed outlier: 4.111A pdb=" N THR A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 4.555A pdb=" N ASP A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 508 through 528 removed outlier: 3.622A pdb=" N VAL A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 535 through 538 Processing helix chain 'A' and resid 539 through 543 239 hydrogen bonds defined for protein. 702 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: 1.87 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3597 1.03 - 1.23: 4 1.23 - 1.42: 1518 1.42 - 1.61: 2079 1.61 - 1.81: 21 Bond restraints: 7219 Sorted by residual: bond pdb=" N ARG A 246 " pdb=" H ARG A 246 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" N ARG A 172 " pdb=" H ARG A 172 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" N PHE A 247 " pdb=" CA PHE A 247 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.20e-02 6.94e+03 4.41e+00 bond pdb=" N PHE A 247 " pdb=" H PHE A 247 " ideal model delta sigma weight residual 0.860 0.901 -0.041 2.00e-02 2.50e+03 4.29e+00 bond pdb=" N ARG A 246 " pdb=" CA ARG A 246 " ideal model delta sigma weight residual 1.461 1.477 -0.016 1.20e-02 6.94e+03 1.78e+00 ... (remaining 7214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 12672 1.34 - 2.67: 384 2.67 - 4.01: 28 4.01 - 5.34: 6 5.34 - 6.68: 3 Bond angle restraints: 13093 Sorted by residual: angle pdb=" CA PHE A 247 " pdb=" C PHE A 247 " pdb=" O PHE A 247 " ideal model delta sigma weight residual 120.90 114.22 6.68 1.07e+00 8.73e-01 3.90e+01 angle pdb=" CA PHE A 247 " pdb=" C PHE A 247 " pdb=" N GLN A 248 " ideal model delta sigma weight residual 116.97 121.01 -4.04 1.20e+00 6.94e-01 1.14e+01 angle pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 121.45 118.13 3.32 1.07e+00 8.73e-01 9.63e+00 angle pdb=" C ARG A 246 " pdb=" CA ARG A 246 " pdb=" CB ARG A 246 " ideal model delta sigma weight residual 110.34 113.96 -3.62 1.40e+00 5.10e-01 6.67e+00 angle pdb=" O PHE A 247 " pdb=" C PHE A 247 " pdb=" N GLN A 248 " ideal model delta sigma weight residual 122.09 124.74 -2.65 1.04e+00 9.25e-01 6.49e+00 ... (remaining 13088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3094 17.21 - 34.41: 209 34.41 - 51.62: 62 51.62 - 68.83: 28 68.83 - 86.04: 13 Dihedral angle restraints: 3406 sinusoidal: 1790 harmonic: 1616 Sorted by residual: dihedral pdb=" CD ARG A 246 " pdb=" NE ARG A 246 " pdb=" CZ ARG A 246 " pdb=" NH1 ARG A 246 " ideal model delta sinusoidal sigma weight residual 0.00 -37.27 37.27 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 130 " pdb=" C ASP A 130 " pdb=" N ALA A 131 " pdb=" CA ALA A 131 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" NE ARG A 246 " pdb=" CZ ARG A 246 " pdb=" NH1 ARG A 246 " pdb="HH12 ARG A 246 " ideal model delta sinusoidal sigma weight residual 0.00 -86.04 86.04 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 3403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 326 0.022 - 0.043: 132 0.043 - 0.065: 73 0.065 - 0.087: 28 0.087 - 0.108: 21 Chirality restraints: 580 Sorted by residual: chirality pdb=" CA VAL A 340 " pdb=" N VAL A 340 " pdb=" C VAL A 340 " pdb=" CB VAL A 340 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA VAL A 255 " pdb=" N VAL A 255 " pdb=" C VAL A 255 " pdb=" CB VAL A 255 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA PRO A 398 " pdb=" N PRO A 398 " pdb=" C PRO A 398 " pdb=" CB PRO A 398 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.82e-01 ... (remaining 577 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 246 " -0.311 9.50e-02 1.11e+02 4.59e-01 4.51e+03 pdb=" NE ARG A 246 " 0.294 2.00e-02 2.50e+03 pdb=" CZ ARG A 246 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 246 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 246 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 246 " -0.878 2.00e-02 2.50e+03 pdb="HH12 ARG A 246 " 0.647 2.00e-02 2.50e+03 pdb="HH21 ARG A 246 " 0.475 2.00e-02 2.50e+03 pdb="HH22 ARG A 246 " -0.538 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 172 " -0.300 9.50e-02 1.11e+02 3.68e-01 2.83e+03 pdb=" NE ARG A 172 " 0.138 2.00e-02 2.50e+03 pdb=" CZ ARG A 172 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 172 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 172 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 172 " 0.722 2.00e-02 2.50e+03 pdb="HH12 ARG A 172 " -0.760 2.00e-02 2.50e+03 pdb="HH21 ARG A 172 " -0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 172 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 168 " -0.018 2.00e-02 2.50e+03 2.09e-02 6.53e+00 pdb=" CG ASN A 168 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 168 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 168 " 0.032 2.00e-02 2.50e+03 pdb="HD21 ASN A 168 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A 168 " -0.031 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 607 2.23 - 2.82: 15978 2.82 - 3.42: 19380 3.42 - 4.01: 25425 4.01 - 4.60: 39837 Nonbonded interactions: 101227 Sorted by model distance: nonbonded pdb=" HG SER A 120 " pdb=" OD1 ASN A 461 " model vdw 1.641 2.450 nonbonded pdb="HD21 ASN A 436 " pdb=" OD1 ASN A 453 " model vdw 1.648 2.450 nonbonded pdb=" O VAL A 176 " pdb=" HG1 THR A 180 " model vdw 1.662 2.450 nonbonded pdb="HE21 GLN A 250 " pdb=" O ARG A 252 " model vdw 1.674 2.450 nonbonded pdb=" O PHE A 268 " pdb=" HG1 THR A 272 " model vdw 1.689 2.450 ... (remaining 101222 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 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: 1.600 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 0.025 3618 Z= 0.135 Angle : 0.526 6.679 4941 Z= 0.304 Chirality : 0.036 0.108 580 Planarity : 0.016 0.296 598 Dihedral : 12.310 73.169 1252 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.01 (0.42), residues: 439 helix: 0.79 (0.29), residues: 335 sheet: None (None), residues: 0 loop : 0.67 (0.70), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.008 0.001 TYR A 448 PHE 0.017 0.001 PHE A 376 TRP 0.011 0.001 TRP A 462 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 3618) covalent geometry : angle 0.52612 / 0.30 ( 4941) hydrogen bonds : bond 0.12176 / 8.04 ( 239) hydrogen bonds : angle 5.79248 / 4.30 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.7339 (tp) cc_final: 0.6762 (mp) REVERT: A 433 MET cc_start: 0.7810 (mmm) cc_final: 0.7518 (mmp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1666 time to fit residues: 10.4985 Evaluate side-chains 46 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.0470 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.142779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.127225 restraints weight = 11865.138| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.47 r_work: 0.3194 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3618 Z= 0.126 Angle : 0.504 5.709 4941 Z= 0.269 Chirality : 0.036 0.108 580 Planarity : 0.005 0.038 598 Dihedral : 4.073 18.535 473 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.79 % Allowed : 5.50 % Favored : 93.72 % 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: 1.56 (0.41), residues: 439 helix: 1.30 (0.29), residues: 331 sheet: None (None), residues: 0 loop : 0.46 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.011 0.001 TYR A 377 PHE 0.016 0.001 PHE A 376 TRP 0.010 0.001 TRP A 462 HIS 0.002 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 3618) covalent geometry : angle 0.50420 / 0.27 ( 4941) hydrogen bonds : bond 0.04314 / 2.69 ( 239) hydrogen bonds : angle 4.32153 / 3.07 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.6309 (tpt170) cc_final: 0.6043 (tpt-90) REVERT: A 300 LEU cc_start: 0.7258 (tp) cc_final: 0.6673 (mp) REVERT: A 433 MET cc_start: 0.7685 (mmm) cc_final: 0.7470 (mmp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.1358 time to fit residues: 8.1552 Evaluate side-chains 46 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 149 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [28, 40, 35, 39, 14, 1, 29, 30, 4, 15, 13] chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.142925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.127834 restraints weight = 11787.315| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.41 r_work: 0.3202 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3618 Z= 0.118 Angle : 0.464 5.733 4941 Z= 0.246 Chirality : 0.036 0.111 580 Planarity : 0.005 0.038 598 Dihedral : 3.887 16.459 473 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % 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: 1.91 (0.41), residues: 439 helix: 1.62 (0.29), residues: 331 sheet: None (None), residues: 0 loop : 0.37 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.010 0.001 TYR A 377 PHE 0.013 0.001 PHE A 376 TRP 0.010 0.001 TRP A 462 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3618) covalent geometry : angle 0.46360 / 0.25 ( 4941) hydrogen bonds : bond 0.03972 / 2.48 ( 239) hydrogen bonds : angle 4.14398 / 2.95 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.6478 (tpt170) cc_final: 0.6272 (tpt-90) REVERT: A 300 LEU cc_start: 0.7251 (tp) cc_final: 0.6674 (mp) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1500 time to fit residues: 7.9214 Evaluate side-chains 42 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [19, 42, 24, 9, 10, 40, 3, 12, 7, 4, 18] chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 40 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.144816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.129902 restraints weight = 11860.112| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.41 r_work: 0.3228 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3618 Z= 0.097 Angle : 0.444 5.744 4941 Z= 0.234 Chirality : 0.035 0.110 580 Planarity : 0.005 0.036 598 Dihedral : 3.702 14.929 473 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.52 % Allowed : 5.76 % Favored : 93.72 % 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: 2.30 (0.41), residues: 439 helix: 1.95 (0.29), residues: 331 sheet: None (None), residues: 0 loop : 0.31 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 252 TYR 0.008 0.001 TYR A 409 PHE 0.012 0.001 PHE A 376 TRP 0.010 0.001 TRP A 462 HIS 0.001 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 3618) covalent geometry : angle 0.44379 / 0.23 ( 4941) hydrogen bonds : bond 0.03662 / 2.30 ( 239) hydrogen bonds : angle 3.92595 / 2.79 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.7228 (tp) cc_final: 0.6633 (mp) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1605 time to fit residues: 8.7603 Evaluate side-chains 40 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [24, 27, 35, 12, 7, 2, 23, 34, 0, 4, 13] chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.142835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.127753 restraints weight = 11946.516| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.43 r_work: 0.3201 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3618 Z= 0.119 Angle : 0.453 5.719 4941 Z= 0.239 Chirality : 0.036 0.112 580 Planarity : 0.005 0.037 598 Dihedral : 3.696 15.480 473 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.52 % Allowed : 6.28 % Favored : 93.19 % 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: 2.36 (0.41), residues: 439 helix: 2.03 (0.29), residues: 331 sheet: None (None), residues: 0 loop : 0.18 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.009 0.001 TYR A 409 PHE 0.013 0.001 PHE A 376 TRP 0.010 0.001 TRP A 462 HIS 0.001 0.000 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3618) covalent geometry : angle 0.45301 / 0.24 ( 4941) hydrogen bonds : bond 0.03732 / 2.33 ( 239) hydrogen bonds : angle 3.93828 / 2.81 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 TRP cc_start: 0.9004 (m100) cc_final: 0.8802 (m100) REVERT: A 300 LEU cc_start: 0.7217 (tp) cc_final: 0.6599 (mp) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1384 time to fit residues: 7.1424 Evaluate side-chains 41 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [37, 8, 3, 10, 32, 5, 34, 26, 17, 24, 42] chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.137400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122984 restraints weight = 12100.217| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.36 r_work: 0.3143 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3618 Z= 0.210 Angle : 0.514 5.712 4941 Z= 0.277 Chirality : 0.039 0.121 580 Planarity : 0.005 0.039 598 Dihedral : 3.987 17.634 473 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.79 % Allowed : 6.54 % Favored : 92.67 % 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: 1.84 (0.40), residues: 439 helix: 1.76 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.26 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.012 0.002 TYR A 411 PHE 0.014 0.002 PHE A 376 TRP 0.012 0.001 TRP A 462 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 3618) covalent geometry : angle 0.51399 / 0.28 ( 4941) hydrogen bonds : bond 0.04188 / 2.61 ( 239) hydrogen bonds : angle 4.18898 / 2.99 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 120 SER cc_start: 0.8698 (m) cc_final: 0.8341 (p) REVERT: A 139 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7893 (ttm-80) REVERT: A 252 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7510 (mtm110) REVERT: A 300 LEU cc_start: 0.7215 (tp) cc_final: 0.6577 (mp) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1408 time to fit residues: 8.7026 Evaluate side-chains 49 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 324 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [17, 15, 0, 25, 12, 22, 30, 26, 9, 28, 34] chunk 17 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.126589 restraints weight = 11857.610| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.39 r_work: 0.3185 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3618 Z= 0.114 Angle : 0.454 5.708 4941 Z= 0.241 Chirality : 0.035 0.113 580 Planarity : 0.005 0.038 598 Dihedral : 3.787 15.470 473 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.79 % Allowed : 7.33 % Favored : 91.88 % 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: 2.21 (0.40), residues: 439 helix: 1.94 (0.29), residues: 331 sheet: None (None), residues: 0 loop : 0.04 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.008 0.001 TYR A 377 PHE 0.013 0.001 PHE A 376 TRP 0.010 0.001 TRP A 462 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 3618) covalent geometry : angle 0.45423 / 0.24 ( 4941) hydrogen bonds : bond 0.03763 / 2.34 ( 239) hydrogen bonds : angle 3.96450 / 2.83 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8663 (m) cc_final: 0.8300 (p) REVERT: A 139 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7862 (ttm-80) REVERT: A 252 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7467 (mtm110) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.1374 time to fit residues: 7.5750 Evaluate side-chains 42 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [9, 34, 40, 20, 0, 28, 22, 27, 30, 18, 37] chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.139029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.124466 restraints weight = 12015.653| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.36 r_work: 0.3158 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3618 Z= 0.163 Angle : 0.482 5.739 4941 Z= 0.258 Chirality : 0.037 0.116 580 Planarity : 0.005 0.039 598 Dihedral : 3.861 16.518 473 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.52 % Allowed : 8.38 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.40), residues: 439 helix: 1.93 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.25 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.010 0.001 TYR A 377 PHE 0.017 0.002 PHE A 376 TRP 0.011 0.001 TRP A 462 HIS 0.007 0.002 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 3618) covalent geometry : angle 0.48235 / 0.26 ( 4941) hydrogen bonds : bond 0.03959 / 2.46 ( 239) hydrogen bonds : angle 4.06332 / 2.91 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8678 (m) cc_final: 0.8303 (p) REVERT: A 139 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7898 (ttm-80) REVERT: A 246 ARG cc_start: 0.6725 (tpt-90) cc_final: 0.6297 (tpt-90) REVERT: A 252 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7485 (mtm110) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1475 time to fit residues: 7.7345 Evaluate side-chains 42 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [42, 15, 11, 16, 14, 12, 5, 8, 4, 43, 0] chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.140393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.125547 restraints weight = 11990.539| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.41 r_work: 0.3169 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3618 Z= 0.126 Angle : 0.459 5.718 4941 Z= 0.244 Chirality : 0.036 0.113 580 Planarity : 0.005 0.038 598 Dihedral : 3.789 15.755 473 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.52 % Allowed : 8.38 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.40), residues: 439 helix: 2.08 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.20 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.009 0.001 TYR A 377 PHE 0.015 0.001 PHE A 376 TRP 0.016 0.001 TRP A 264 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3618) covalent geometry : angle 0.45867 / 0.24 ( 4941) hydrogen bonds : bond 0.03786 / 2.37 ( 239) hydrogen bonds : angle 3.97114 / 2.85 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8677 (m) cc_final: 0.8320 (p) REVERT: A 139 ARG cc_start: 0.8210 (ttt180) cc_final: 0.7935 (ttm-80) REVERT: A 246 ARG cc_start: 0.6821 (tpt-90) cc_final: 0.6409 (tpt-90) REVERT: A 252 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7540 (mtm110) outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1609 time to fit residues: 8.3583 Evaluate side-chains 39 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [32, 6, 24, 18, 7, 19, 22, 38, 8, 5, 11] chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.139635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.124940 restraints weight = 11903.580| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.38 r_work: 0.3162 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3618 Z= 0.141 Angle : 0.468 5.715 4941 Z= 0.249 Chirality : 0.036 0.113 580 Planarity : 0.005 0.040 598 Dihedral : 3.811 16.070 473 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.52 % Allowed : 7.85 % Favored : 91.62 % 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: 2.15 (0.40), residues: 439 helix: 2.01 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.26 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.009 0.001 TYR A 377 PHE 0.015 0.002 PHE A 376 TRP 0.018 0.001 TRP A 264 HIS 0.004 0.002 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 3618) covalent geometry : angle 0.46786 / 0.25 ( 4941) hydrogen bonds : bond 0.03841 / 2.39 ( 239) hydrogen bonds : angle 4.00080 / 2.86 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8689 (m) cc_final: 0.8331 (p) REVERT: A 139 ARG cc_start: 0.8218 (ttt180) cc_final: 0.7943 (ttm-80) REVERT: A 246 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6397 (tpt-90) REVERT: A 252 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7541 (mtm110) REVERT: A 401 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7166 (mm-30) outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1566 time to fit residues: 8.1581 Evaluate side-chains 41 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 302 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [19, 33, 3, 13, 28, 18, 43, 7, 1, 6, 34] chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.141438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127022 restraints weight = 11805.487| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.36 r_work: 0.3195 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3618 Z= 0.108 Angle : 0.446 5.711 4941 Z= 0.236 Chirality : 0.036 0.113 580 Planarity : 0.005 0.038 598 Dihedral : 3.715 15.132 473 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.52 % Allowed : 8.12 % Favored : 91.36 % 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: 2.41 (0.41), residues: 439 helix: 2.22 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.22 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.008 0.001 TYR A 377 PHE 0.015 0.001 PHE A 376 TRP 0.015 0.001 TRP A 264 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 3618) covalent geometry : angle 0.44610 / 0.24 ( 4941) hydrogen bonds : bond 0.03656 / 2.30 ( 239) hydrogen bonds : angle 3.89255 / 2.79 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.84 seconds wall clock time: 34 minutes 1.36 seconds (2041.36 seconds total)