Starting phenix.real_space_refine on Tue Aug 4 13:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2026/8ws7_37800.cif" } resolution = 3.26 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= 0.001 sd= 0.015 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 P 54 5.49 5 S 3 5.16 5 C 1934 2.51 5 N 604 2.21 5 O 738 1.98 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3333 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 627 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 23} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.06, per 1000 atoms: 0.32 Number of scatterers: 3333 At special positions: 0 Unit cell: (54.78, 77.88, 91.08, 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 3 16.00 P 54 15.00 O 738 8.00 N 604 7.00 C 1934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 89.4 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 38.0% alpha, 7.9% beta 9 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.087A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.654A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 158 removed outlier: 3.582A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.534A pdb=" N ARG A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.559A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.684A pdb=" N ILE A 198 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 296 " --> pdb=" O MET A 307 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.48 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 774 1.33 - 1.45: 971 1.45 - 1.57: 1670 1.57 - 1.69: 105 1.69 - 1.81: 4 Bond restraints: 3524 Sorted by residual: bond pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 1.522 1.561 -0.039 1.06e-02 8.90e+03 1.33e+01 bond pdb=" C3' DA C -10 " pdb=" C2' DA C -10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT C -7 " pdb=" C2' DT C -7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.87e+00 bond pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.01e-02 9.80e+03 7.89e+00 ... (remaining 3519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4660 1.45 - 2.90: 317 2.90 - 4.35: 32 4.35 - 5.80: 4 5.80 - 7.25: 2 Bond angle restraints: 5015 Sorted by residual: angle pdb=" O5' C B -6 " pdb=" C5' C B -6 " pdb=" C4' C B -6 " ideal model delta sigma weight residual 109.40 112.97 -3.57 8.00e-01 1.56e+00 1.99e+01 angle pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sigma weight residual 117.70 122.74 -5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 ... (remaining 5010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 1926 34.05 - 68.10: 172 68.10 - 102.14: 17 102.14 - 136.19: 0 136.19 - 170.24: 2 Dihedral angle restraints: 2117 sinusoidal: 1322 harmonic: 795 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 58.25 141.75 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 61.76 170.24 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA TRP A 318 " pdb=" C TRP A 318 " pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 2114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 432 0.052 - 0.103: 85 0.103 - 0.155: 51 0.155 - 0.206: 1 0.206 - 0.258: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 198 " pdb=" N ILE A 198 " pdb=" C ILE A 198 " pdb=" CB ILE A 198 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS A 273 " pdb=" N LYS A 273 " pdb=" C LYS A 273 " pdb=" CB LYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 568 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 70 " -0.040 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 71 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 69 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER A 69 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 69 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 70 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 76 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.025 5.00e-02 4.00e+02 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 809 2.80 - 3.32: 2904 3.32 - 3.85: 5913 3.85 - 4.37: 7050 4.37 - 4.90: 10629 Nonbonded interactions: 27305 Sorted by model distance: nonbonded pdb=" NE2 GLN A 127 " pdb=" O4 DT D -2 " model vdw 2.272 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.314 3.120 nonbonded pdb=" O2' C B -6 " pdb=" OP2 C B -5 " model vdw 2.334 3.040 nonbonded pdb=" O6 DG C 5 " pdb=" N4 DC D -6 " model vdw 2.371 3.120 nonbonded pdb=" N6 DA C -10 " pdb=" O4 U B 10 " model vdw 2.425 3.120 ... (remaining 27300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.600 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.004 0.039 3524 Z= 0.345 Angle : 0.762 7.250 5015 Z= 0.576 Chirality : 0.054 0.258 571 Planarity : 0.006 0.062 450 Dihedral : 21.449 170.241 1609 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 1.72 % Favored : 97.41 % 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: -1.30 (0.50), residues: 275 helix: -1.23 (0.51), residues: 98 sheet: 0.58 (1.11), residues: 26 loop : -0.78 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.006 0.001 TYR A 201 PHE 0.009 0.001 PHE A 334 TRP 0.013 0.002 TRP A 318 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.34 ( 3524) covalent geometry : angle 0.76194 / 0.58 ( 5015) hydrogen bonds : bond 0.25870 / 17.40 ( 94) hydrogen bonds : angle 9.73398 / 6.85 ( 247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.093 Fit side-chains REVERT: A 74 GLU cc_start: 0.6450 (mp0) cc_final: 0.6114 (mp0) REVERT: A 302 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7762 (mtpp) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1605 time to fit residues: 5.5251 Evaluate side-chains 26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.140807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125622 restraints weight = 4848.985| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.31 r_work: 0.3492 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3524 Z= 0.252 Angle : 0.727 9.038 5015 Z= 0.400 Chirality : 0.050 0.199 571 Planarity : 0.007 0.046 450 Dihedral : 24.034 172.841 1055 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 7.76 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.48), residues: 275 helix: -1.05 (0.48), residues: 100 sheet: -0.25 (1.06), residues: 28 loop : -0.73 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 260 TYR 0.009 0.002 TYR A 89 PHE 0.022 0.003 PHE A 350 TRP 0.019 0.003 TRP A 112 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 ( 3524) covalent geometry : angle 0.72684 / 0.40 ( 5015) hydrogen bonds : bond 0.06934 / 4.61 ( 94) hydrogen bonds : angle 5.81003 / 4.05 ( 247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.096 Fit side-chains REVERT: A 74 GLU cc_start: 0.7110 (mp0) cc_final: 0.6668 (mp0) REVERT: A 155 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6860 (ttp-170) REVERT: A 302 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8274 (mtpp) REVERT: A 330 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6939 (tm-30) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.1497 time to fit residues: 6.2011 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.141284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126078 restraints weight = 4974.617| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.34 r_work: 0.3474 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3524 Z= 0.221 Angle : 0.672 7.785 5015 Z= 0.374 Chirality : 0.047 0.166 571 Planarity : 0.006 0.046 450 Dihedral : 23.910 173.301 1055 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.59 % Allowed : 10.78 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.47), residues: 275 helix: -0.80 (0.49), residues: 102 sheet: -0.58 (1.01), residues: 28 loop : -0.78 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 271 TYR 0.007 0.002 TYR A 201 PHE 0.019 0.003 PHE A 350 TRP 0.018 0.002 TRP A 112 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 ( 3524) covalent geometry : angle 0.67224 / 0.37 ( 5015) hydrogen bonds : bond 0.06036 / 4.16 ( 94) hydrogen bonds : angle 5.28201 / 3.70 ( 247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.101 Fit side-chains REVERT: A 74 GLU cc_start: 0.7167 (mp0) cc_final: 0.6709 (mp0) REVERT: A 155 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6893 (ttp-170) REVERT: A 302 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8325 (mtpp) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.1618 time to fit residues: 6.1115 Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 3 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 overall best weight: 0.1476 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.145680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130452 restraints weight = 4803.356| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.31 r_work: 0.3556 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3524 Z= 0.128 Angle : 0.575 7.420 5015 Z= 0.325 Chirality : 0.041 0.147 571 Planarity : 0.005 0.037 450 Dihedral : 23.669 174.486 1055 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.45 % Allowed : 12.93 % Favored : 83.62 % 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: -0.73 (0.49), residues: 275 helix: -0.16 (0.51), residues: 104 sheet: -0.53 (0.88), residues: 33 loop : -0.62 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.012 0.001 TYR A 89 PHE 0.010 0.001 PHE A 334 TRP 0.018 0.002 TRP A 318 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 3524) covalent geometry : angle 0.57521 / 0.33 ( 5015) hydrogen bonds : bond 0.04983 / 3.44 ( 94) hydrogen bonds : angle 4.71003 / 3.26 ( 247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.099 Fit side-chains REVERT: A 74 GLU cc_start: 0.6975 (mp0) cc_final: 0.6543 (mp0) REVERT: A 190 GLU cc_start: 0.6488 (mp0) cc_final: 0.6130 (mt-10) REVERT: A 302 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8167 (mtpp) outliers start: 8 outliers final: 1 residues processed: 36 average time/residue: 0.1638 time to fit residues: 6.6159 Evaluate side-chains 30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.141642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126297 restraints weight = 4844.027| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.32 r_work: 0.3496 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3524 Z= 0.194 Angle : 0.635 10.853 5015 Z= 0.346 Chirality : 0.045 0.165 571 Planarity : 0.006 0.041 450 Dihedral : 23.564 174.081 1051 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.02 % Allowed : 14.66 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.48), residues: 275 helix: -0.26 (0.50), residues: 102 sheet: -0.67 (0.89), residues: 33 loop : -0.63 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 314 TYR 0.011 0.002 TYR A 89 PHE 0.018 0.003 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 ( 3524) covalent geometry : angle 0.63535 / 0.35 ( 5015) hydrogen bonds : bond 0.05221 / 3.60 ( 94) hydrogen bonds : angle 4.92733 / 3.41 ( 247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.059 Fit side-chains REVERT: A 74 GLU cc_start: 0.7127 (mp0) cc_final: 0.6718 (mp0) REVERT: A 302 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8322 (mtpp) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.1264 time to fit residues: 4.6481 Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.0970 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0050 overall best weight: 0.1530 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.145450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129858 restraints weight = 4804.758| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.33 r_work: 0.3544 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3524 Z= 0.120 Angle : 0.552 8.020 5015 Z= 0.309 Chirality : 0.040 0.151 571 Planarity : 0.005 0.037 450 Dihedral : 23.500 175.565 1051 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.16 % Allowed : 17.67 % Favored : 80.17 % 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: -0.47 (0.50), residues: 275 helix: 0.16 (0.52), residues: 102 sheet: -0.61 (0.85), residues: 33 loop : -0.48 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.008 0.001 TYR A 89 PHE 0.010 0.001 PHE A 350 TRP 0.015 0.001 TRP A 318 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 3524) covalent geometry : angle 0.55239 / 0.31 ( 5015) hydrogen bonds : bond 0.04425 / 3.05 ( 94) hydrogen bonds : angle 4.64528 / 3.20 ( 247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.089 Fit side-chains REVERT: A 74 GLU cc_start: 0.7040 (mp0) cc_final: 0.6609 (mp0) REVERT: A 190 GLU cc_start: 0.6425 (mp0) cc_final: 0.6113 (mt-10) REVERT: A 302 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8125 (mtpp) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.0942 time to fit residues: 3.4567 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.142556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126829 restraints weight = 4915.006| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.35 r_work: 0.3479 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3524 Z= 0.172 Angle : 0.584 7.291 5015 Z= 0.321 Chirality : 0.042 0.159 571 Planarity : 0.006 0.039 450 Dihedral : 23.503 175.406 1051 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.88 % Allowed : 15.95 % Favored : 80.17 % 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: -0.54 (0.49), residues: 275 helix: 0.16 (0.51), residues: 102 sheet: -0.72 (0.88), residues: 33 loop : -0.56 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.008 0.002 TYR A 201 PHE 0.014 0.002 PHE A 350 TRP 0.014 0.002 TRP A 112 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 3524) covalent geometry : angle 0.58445 / 0.32 ( 5015) hydrogen bonds : bond 0.04750 / 3.29 ( 94) hydrogen bonds : angle 4.72138 / 3.29 ( 247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.054 Fit side-chains REVERT: A 74 GLU cc_start: 0.7148 (mp0) cc_final: 0.6677 (mp0) REVERT: A 302 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8269 (mtpp) REVERT: A 332 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6494 (mt) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 0.0714 time to fit residues: 2.6329 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.143164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127705 restraints weight = 4869.008| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.32 r_work: 0.3519 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3524 Z= 0.148 Angle : 0.574 8.007 5015 Z= 0.314 Chirality : 0.042 0.155 571 Planarity : 0.006 0.044 450 Dihedral : 23.532 175.850 1051 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.02 % Allowed : 16.81 % Favored : 80.17 % 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: -0.43 (0.49), residues: 275 helix: 0.29 (0.51), residues: 102 sheet: -0.74 (0.89), residues: 33 loop : -0.51 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.014 0.002 PHE A 350 TRP 0.013 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 3524) covalent geometry : angle 0.57382 / 0.31 ( 5015) hydrogen bonds : bond 0.04552 / 3.13 ( 94) hydrogen bonds : angle 4.71241 / 3.29 ( 247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.065 Fit side-chains REVERT: A 74 GLU cc_start: 0.7120 (mp0) cc_final: 0.6641 (mp0) REVERT: A 190 GLU cc_start: 0.6423 (mp0) cc_final: 0.6129 (mt-10) REVERT: A 302 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8231 (mtpp) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.0777 time to fit residues: 3.1916 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.142152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126297 restraints weight = 4892.584| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.35 r_work: 0.3490 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3524 Z= 0.165 Angle : 0.570 8.295 5015 Z= 0.315 Chirality : 0.042 0.157 571 Planarity : 0.006 0.040 450 Dihedral : 23.594 176.214 1051 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.88 % Allowed : 16.81 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.49), residues: 275 helix: 0.26 (0.51), residues: 104 sheet: -0.79 (0.89), residues: 33 loop : -0.62 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.008 0.002 TYR A 201 PHE 0.014 0.002 PHE A 350 TRP 0.014 0.002 TRP A 112 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 3524) covalent geometry : angle 0.57032 / 0.32 ( 5015) hydrogen bonds : bond 0.04577 / 3.15 ( 94) hydrogen bonds : angle 4.66255 / 3.31 ( 247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.057 Fit side-chains REVERT: A 74 GLU cc_start: 0.7115 (mp0) cc_final: 0.6616 (mp0) REVERT: A 190 GLU cc_start: 0.6415 (mp0) cc_final: 0.6117 (mt-10) REVERT: A 280 LEU cc_start: 0.6621 (mm) cc_final: 0.6405 (tp) REVERT: A 302 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8275 (mtpp) REVERT: A 330 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7001 (tm-30) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.0724 time to fit residues: 3.3269 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 19 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.142908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127038 restraints weight = 4886.946| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.32 r_work: 0.3512 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3524 Z= 0.145 Angle : 0.569 8.202 5015 Z= 0.315 Chirality : 0.040 0.151 571 Planarity : 0.005 0.039 450 Dihedral : 23.592 176.925 1051 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.31 % Allowed : 17.24 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.50), residues: 275 helix: 0.41 (0.51), residues: 104 sheet: -0.78 (0.87), residues: 33 loop : -0.53 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.012 0.002 PHE A 350 TRP 0.013 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 3524) covalent geometry : angle 0.56888 / 0.32 ( 5015) hydrogen bonds : bond 0.04447 / 3.10 ( 94) hydrogen bonds : angle 4.58304 / 3.26 ( 247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.096 Fit side-chains REVERT: A 74 GLU cc_start: 0.7084 (mp0) cc_final: 0.6594 (mp0) REVERT: A 190 GLU cc_start: 0.6401 (mp0) cc_final: 0.6105 (mt-10) REVERT: A 280 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6482 (tp) REVERT: A 302 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8229 (mtpp) REVERT: A 330 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7009 (tm-30) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.0864 time to fit residues: 3.8284 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.2130 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128051 restraints weight = 4879.500| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.33 r_work: 0.3528 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3524 Z= 0.124 Angle : 0.551 7.830 5015 Z= 0.306 Chirality : 0.039 0.150 571 Planarity : 0.005 0.039 450 Dihedral : 23.560 177.441 1051 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.45 % Allowed : 18.53 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.50), residues: 275 helix: 0.59 (0.52), residues: 104 sheet: -0.69 (0.87), residues: 33 loop : -0.49 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.010 0.001 PHE A 350 TRP 0.014 0.001 TRP A 318 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3524) covalent geometry : angle 0.55062 / 0.31 ( 5015) hydrogen bonds : bond 0.04286 / 3.02 ( 94) hydrogen bonds : angle 4.51236 / 3.20 ( 247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 942.29 seconds wall clock time: 16 minutes 47.54 seconds (1007.54 seconds total)