Starting phenix.real_space_refine on Tue Feb 3 20:36:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h62_51895/02_2026/9h62_51895.map" } resolution = 3.43 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= 0.013 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 2 4.86 5 C 2215 2.51 5 N 522 2.21 5 O 553 1.98 5 H 3307 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6619 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6597 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 22 Unusual residues: {'CFA': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Time building chain proxies: 1.16, per 1000 atoms: 0.18 Number of scatterers: 6619 At special positions: 0 Unit cell: (78.287, 60.818, 70.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 20 16.00 O 553 8.00 N 522 7.00 C 2215 6.00 H 3307 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 465 " distance=2.04 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: 0.41 Conformation dependent library (CDL) restraints added in 180.2 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 60 through 73 removed outlier: 4.036A pdb=" N THR A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.539A pdb=" N GLN A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 3.712A pdb=" N GLU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 129 through 161 removed outlier: 3.692A pdb=" N TYR A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 181 through 184 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 217 removed outlier: 4.296A pdb=" N GLY A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.687A pdb=" N PHE A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.968A pdb=" N ALA A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 290 removed outlier: 3.830A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.159A pdb=" N LEU A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 303' Processing helix chain 'A' and resid 306 through 340 Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.614A pdb=" N VAL A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.689A pdb=" N ILE A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 417 through 436 removed outlier: 3.611A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 229 hydrogen bonds defined for protein. 681 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: 1.00 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3301 1.04 - 1.23: 63 1.23 - 1.43: 1453 1.43 - 1.63: 1873 1.63 - 1.83: 34 Bond restraints: 6724 Sorted by residual: bond pdb=" C1' CFA A 500 " pdb=" O1' CFA A 500 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C2' CFA A 500 " pdb="CL3 CFA A 500 " ideal model delta sigma weight residual 1.727 1.784 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C4' CFA A 500 " pdb="CL4 CFA A 500 " ideal model delta sigma weight residual 1.733 1.783 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" N GLY A 44 " pdb=" CA GLY A 44 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.09e+00 bond pdb=" N GLY A 44 " pdb=" H GLY A 44 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 6719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11985 1.65 - 3.29: 102 3.29 - 4.94: 8 4.94 - 6.59: 1 6.59 - 8.23: 2 Bond angle restraints: 12098 Sorted by residual: angle pdb=" O1 CFA A 500 " pdb=" C1 CFA A 500 " pdb=" O2 CFA A 500 " ideal model delta sigma weight residual 128.33 120.10 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" C2 CFA A 500 " pdb=" C1 CFA A 500 " pdb=" O1 CFA A 500 " ideal model delta sigma weight residual 113.24 119.85 -6.61 3.00e+00 1.11e-01 4.85e+00 angle pdb=" C6' CFA A 500 " pdb=" C1' CFA A 500 " pdb=" O1' CFA A 500 " ideal model delta sigma weight residual 125.40 119.35 6.05 3.00e+00 1.11e-01 4.07e+00 angle pdb=" C1' CFA A 500 " pdb=" O1' CFA A 500 " pdb=" C2 CFA A 500 " ideal model delta sigma weight residual 118.82 114.21 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CA GLY A 44 " pdb=" N GLY A 44 " pdb=" H GLY A 44 " ideal model delta sigma weight residual 114.00 109.45 4.55 3.00e+00 1.11e-01 2.30e+00 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2769 16.30 - 32.60: 289 32.60 - 48.91: 83 48.91 - 65.21: 41 65.21 - 81.51: 9 Dihedral angle restraints: 3191 sinusoidal: 1624 harmonic: 1567 Sorted by residual: dihedral pdb=" CB CYS A 462 " pdb=" SG CYS A 462 " pdb=" SG CYS A 465 " pdb=" CB CYS A 465 " ideal model delta sinusoidal sigma weight residual -86.00 -6.65 -79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CA ILE A 253 " pdb=" CB ILE A 253 " pdb=" CG1 ILE A 253 " pdb=" CD1 ILE A 253 " ideal model delta sinusoidal sigma weight residual 180.00 123.84 56.16 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB MET A 396 " pdb=" CG MET A 396 " pdb=" SD MET A 396 " pdb=" CE MET A 396 " ideal model delta sinusoidal sigma weight residual 60.00 7.28 52.72 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 3188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 350 0.027 - 0.055: 108 0.055 - 0.082: 43 0.082 - 0.109: 20 0.109 - 0.136: 2 Chirality restraints: 523 Sorted by residual: chirality pdb=" CA ILE A 185 " pdb=" N ILE A 185 " pdb=" C ILE A 185 " pdb=" CB ILE A 185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA PRO A 280 " pdb=" N PRO A 280 " pdb=" C PRO A 280 " pdb=" CB PRO A 280 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 520 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 359 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 360 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 355 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 356 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 372 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 373 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.015 5.00e-02 4.00e+02 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.49: 4556 2.49 - 3.02: 15239 3.02 - 3.54: 18557 3.54 - 4.07: 23225 4.07 - 4.60: 34983 Nonbonded interactions: 96560 Sorted by model distance: nonbonded pdb="HE21 GLN A 60 " pdb="HD22 ASN A 375 " model vdw 1.960 2.100 nonbonded pdb=" H VAL A 450 " pdb="HG21 VAL A 450 " model vdw 1.961 2.270 nonbonded pdb=" H MET A 201 " pdb=" HG3 MET A 201 " model vdw 1.964 2.270 nonbonded pdb=" HD3 ARG A 411 " pdb="HH11 ARG A 411 " model vdw 1.967 2.270 nonbonded pdb=" H THR A 295 " pdb=" HG1 THR A 295 " model vdw 1.968 2.100 ... (remaining 96555 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: 3.400 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: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.650 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.067 3418 Z= 0.137 Angle : 0.469 8.235 4663 Z= 0.233 Chirality : 0.034 0.136 523 Planarity : 0.003 0.029 562 Dihedral : 15.813 81.512 1147 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.57 % Allowed : 17.43 % Favored : 82.00 % 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: 2.70 (0.44), residues: 406 helix: 2.26 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 0.19 (0.74), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 411 TYR 0.007 0.001 TYR A 267 PHE 0.006 0.001 PHE A 175 TRP 0.002 0.000 TRP A 171 HIS 0.002 0.000 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3417) covalent geometry : angle 0.46107 ( 4661) SS BOND : bond 0.01091 ( 1) SS BOND : angle 4.28622 ( 2) hydrogen bonds : bond 0.10663 ( 229) hydrogen bonds : angle 4.31777 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 420 MET cc_start: 0.8320 (tmm) cc_final: 0.7987 (tmm) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.0674 time to fit residues: 5.7091 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.165228 restraints weight = 11525.667| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.24 r_work: 0.3707 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3418 Z= 0.140 Angle : 0.458 4.612 4663 Z= 0.247 Chirality : 0.035 0.124 523 Planarity : 0.003 0.030 562 Dihedral : 4.155 38.303 447 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.86 % Allowed : 16.86 % Favored : 82.29 % 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 (0.44), residues: 406 helix: 2.06 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -0.19 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 451 TYR 0.009 0.001 TYR A 267 PHE 0.008 0.001 PHE A 121 TRP 0.004 0.001 TRP A 171 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3417) covalent geometry : angle 0.44878 ( 4661) SS BOND : bond 0.01044 ( 1) SS BOND : angle 4.37700 ( 2) hydrogen bonds : bond 0.03870 ( 229) hydrogen bonds : angle 3.88400 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.111 Fit side-chains REVERT: A 211 ILE cc_start: 0.8748 (mt) cc_final: 0.8471 (pt) REVERT: A 420 MET cc_start: 0.8313 (tmm) cc_final: 0.8004 (tmm) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.0590 time to fit residues: 5.0956 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162700 restraints weight = 11467.327| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.26 r_work: 0.3682 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3418 Z= 0.149 Angle : 0.460 4.559 4663 Z= 0.249 Chirality : 0.036 0.123 523 Planarity : 0.003 0.032 562 Dihedral : 3.718 25.230 445 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.14 % Allowed : 17.43 % Favored : 81.43 % 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: 2.07 (0.44), residues: 406 helix: 1.89 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.50 (0.71), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 354 TYR 0.008 0.001 TYR A 267 PHE 0.008 0.001 PHE A 121 TRP 0.004 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3417) covalent geometry : angle 0.45144 ( 4661) SS BOND : bond 0.01066 ( 1) SS BOND : angle 4.35537 ( 2) hydrogen bonds : bond 0.03824 ( 229) hydrogen bonds : angle 3.93746 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8764 (mt) cc_final: 0.8463 (pt) REVERT: A 420 MET cc_start: 0.8301 (tmm) cc_final: 0.8002 (tmm) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.0627 time to fit residues: 5.5954 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.187310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160028 restraints weight = 11609.954| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.21 r_work: 0.3672 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3418 Z= 0.175 Angle : 0.482 4.371 4663 Z= 0.264 Chirality : 0.037 0.122 523 Planarity : 0.004 0.035 562 Dihedral : 3.852 21.193 445 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.86 % Allowed : 16.86 % Favored : 82.29 % 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: 1.79 (0.43), residues: 406 helix: 1.69 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.60 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.010 0.001 TYR A 267 PHE 0.009 0.001 PHE A 121 TRP 0.005 0.001 TRP A 443 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3417) covalent geometry : angle 0.47519 ( 4661) SS BOND : bond 0.01263 ( 1) SS BOND : angle 4.02001 ( 2) hydrogen bonds : bond 0.03900 ( 229) hydrogen bonds : angle 3.98856 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.108 Fit side-chains REVERT: A 420 MET cc_start: 0.8308 (tmm) cc_final: 0.7976 (tmm) outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 0.0663 time to fit residues: 5.7227 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.182746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155319 restraints weight = 11415.136| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.17 r_work: 0.3681 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3418 Z= 0.148 Angle : 0.467 4.482 4663 Z= 0.253 Chirality : 0.036 0.123 523 Planarity : 0.004 0.035 562 Dihedral : 3.769 16.954 445 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.43 % Allowed : 16.86 % Favored : 81.71 % 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: 1.79 (0.43), residues: 406 helix: 1.68 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.56 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 133 TYR 0.010 0.001 TYR A 267 PHE 0.008 0.001 PHE A 234 TRP 0.005 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3417) covalent geometry : angle 0.45855 ( 4661) SS BOND : bond 0.01169 ( 1) SS BOND : angle 4.28317 ( 2) hydrogen bonds : bond 0.03757 ( 229) hydrogen bonds : angle 4.00900 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.116 Fit side-chains REVERT: A 420 MET cc_start: 0.8269 (tmm) cc_final: 0.7940 (tmm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.0655 time to fit residues: 5.7363 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160836 restraints weight = 11497.684| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.25 r_work: 0.3683 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3418 Z= 0.126 Angle : 0.454 4.341 4663 Z= 0.245 Chirality : 0.035 0.124 523 Planarity : 0.003 0.035 562 Dihedral : 3.696 15.067 445 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.43 % Allowed : 17.43 % Favored : 81.14 % 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: 1.89 (0.44), residues: 406 helix: 1.75 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.52 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.009 0.001 TYR A 267 PHE 0.007 0.001 PHE A 234 TRP 0.004 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3417) covalent geometry : angle 0.44563 ( 4661) SS BOND : bond 0.01079 ( 1) SS BOND : angle 4.29657 ( 2) hydrogen bonds : bond 0.03606 ( 229) hydrogen bonds : angle 3.95651 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.126 Fit side-chains REVERT: A 420 MET cc_start: 0.8262 (tmm) cc_final: 0.7937 (tmm) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.0501 time to fit residues: 4.4282 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.181592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154350 restraints weight = 11205.499| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.14 r_work: 0.3635 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3418 Z= 0.165 Angle : 0.475 4.393 4663 Z= 0.259 Chirality : 0.036 0.123 523 Planarity : 0.004 0.048 562 Dihedral : 3.760 14.683 445 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.43 % Allowed : 17.14 % Favored : 81.43 % 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: 1.70 (0.43), residues: 406 helix: 1.63 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.64 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 414 TYR 0.010 0.001 TYR A 267 PHE 0.009 0.001 PHE A 234 TRP 0.005 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3417) covalent geometry : angle 0.46656 ( 4661) SS BOND : bond 0.01113 ( 1) SS BOND : angle 4.29328 ( 2) hydrogen bonds : bond 0.03808 ( 229) hydrogen bonds : angle 4.05196 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.167 Fit side-chains REVERT: A 420 MET cc_start: 0.8225 (tmm) cc_final: 0.7880 (tmm) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.0563 time to fit residues: 4.9416 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.191489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165549 restraints weight = 11168.307| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.14 r_work: 0.3814 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3418 Z= 0.100 Angle : 0.443 4.373 4663 Z= 0.237 Chirality : 0.034 0.124 523 Planarity : 0.004 0.052 562 Dihedral : 3.605 13.525 445 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.86 % Allowed : 17.14 % Favored : 82.00 % 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: 2.05 (0.44), residues: 406 helix: 1.82 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -0.27 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 411 TYR 0.009 0.001 TYR A 267 PHE 0.007 0.001 PHE A 146 TRP 0.004 0.000 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3417) covalent geometry : angle 0.43348 ( 4661) SS BOND : bond 0.01052 ( 1) SS BOND : angle 4.33570 ( 2) hydrogen bonds : bond 0.03454 ( 229) hydrogen bonds : angle 3.93229 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.099 Fit side-chains REVERT: A 420 MET cc_start: 0.8300 (tmm) cc_final: 0.7986 (tmm) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.0551 time to fit residues: 4.8130 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.189473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163064 restraints weight = 11230.548| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.16 r_work: 0.3712 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3418 Z= 0.152 Angle : 0.464 4.341 4663 Z= 0.252 Chirality : 0.036 0.124 523 Planarity : 0.004 0.047 562 Dihedral : 3.666 13.644 445 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 17.71 % Favored : 81.14 % 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 (0.44), residues: 406 helix: 1.71 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.53 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 414 TYR 0.010 0.001 TYR A 267 PHE 0.009 0.001 PHE A 121 TRP 0.004 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3417) covalent geometry : angle 0.45533 ( 4661) SS BOND : bond 0.01120 ( 1) SS BOND : angle 4.29295 ( 2) hydrogen bonds : bond 0.03675 ( 229) hydrogen bonds : angle 4.01328 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.182 Fit side-chains REVERT: A 420 MET cc_start: 0.8274 (tmm) cc_final: 0.7960 (tmm) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.0619 time to fit residues: 5.4693 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.189170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163144 restraints weight = 11114.518| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.14 r_work: 0.3719 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3418 Z= 0.141 Angle : 0.463 4.303 4663 Z= 0.252 Chirality : 0.036 0.124 523 Planarity : 0.004 0.049 562 Dihedral : 3.677 14.082 445 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.43 % Allowed : 17.14 % Favored : 81.43 % 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: 1.81 (0.43), residues: 406 helix: 1.70 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.56 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 133 TYR 0.010 0.001 TYR A 99 PHE 0.008 0.001 PHE A 234 TRP 0.004 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3417) covalent geometry : angle 0.45491 ( 4661) SS BOND : bond 0.01096 ( 1) SS BOND : angle 4.27885 ( 2) hydrogen bonds : bond 0.03652 ( 229) hydrogen bonds : angle 4.00261 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.107 Fit side-chains REVERT: A 420 MET cc_start: 0.8282 (tmm) cc_final: 0.7972 (tmm) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0770 time to fit residues: 6.6405 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.161947 restraints weight = 11114.092| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.08 r_work: 0.3704 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3418 Z= 0.165 Angle : 0.475 4.292 4663 Z= 0.261 Chirality : 0.036 0.123 523 Planarity : 0.004 0.047 562 Dihedral : 3.721 13.938 445 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 17.71 % Favored : 81.14 % 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: 1.72 (0.43), residues: 406 helix: 1.61 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.51 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.010 0.001 TYR A 267 PHE 0.010 0.001 PHE A 289 TRP 0.004 0.001 TRP A 443 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3417) covalent geometry : angle 0.46816 ( 4661) SS BOND : bond 0.01355 ( 1) SS BOND : angle 3.98930 ( 2) hydrogen bonds : bond 0.03781 ( 229) hydrogen bonds : angle 4.06592 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.43 seconds wall clock time: 28 minutes 16.15 seconds (1696.15 seconds total)