Starting phenix.real_space_refine on Fri Aug 22 13:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_37800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_37800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_37800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_37800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws7_37800/08_2025/8ws7_37800.map" } 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-2.0-5787/lib/python3.9/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: 1.21, per 1000 atoms: 0.36 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: 0.33 Conformation dependent library (CDL) restraints added in 99.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 0.43 Time building geometry restraints manager: 0.40 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=" 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 bond pdb=" C ARG A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.22e-02 6.72e+03 7.24e+00 bond pdb=" C LYS A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.333 1.366 -0.032 1.44e-02 4.82e+03 5.08e+00 bond pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.19e-02 7.06e+03 1.84e+00 ... (remaining 3519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4796 1.45 - 2.90: 185 2.90 - 4.35: 28 4.35 - 5.80: 4 5.80 - 7.25: 2 Bond angle restraints: 5015 Sorted by residual: angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 113.01 117.65 -4.64 1.20e+00 6.94e-01 1.50e+01 angle pdb=" C ARG A 70 " pdb=" CA ARG A 70 " pdb=" CB ARG A 70 " ideal model delta sigma weight residual 109.22 113.64 -4.42 1.52e+00 4.33e-01 8.47e+00 angle pdb=" CA SER A 69 " pdb=" C SER A 69 " pdb=" N ARG A 70 " ideal model delta sigma weight residual 117.17 114.05 3.12 1.18e+00 7.18e-01 6.97e+00 angle pdb=" O SER A 69 " pdb=" C SER A 69 " pdb=" N ARG A 70 " ideal model delta sigma weight residual 122.09 124.72 -2.63 1.08e+00 8.57e-01 5.92e+00 angle pdb=" N TYR A 140 " pdb=" CA TYR A 140 " pdb=" C TYR A 140 " ideal model delta sigma weight residual 111.07 108.81 2.26 1.07e+00 8.73e-01 4.46e+00 ... (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: 484 0.052 - 0.103: 62 0.103 - 0.155: 22 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: 3.830 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 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= 0.196 Angle : 0.646 7.250 5015 Z= 0.370 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00352 ( 3524) covalent geometry : angle 0.64627 ( 5015) hydrogen bonds : bond 0.25870 ( 94) hydrogen bonds : angle 9.73398 ( 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 : 0.100 Fit side-chains REVERT: A 74 GLU cc_start: 0.6449 (mp0) cc_final: 0.6114 (mp0) REVERT: A 302 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7761 (mtpp) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1464 time to fit residues: 4.9846 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 : 0.059 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125142 restraints weight = 4856.632| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.32 r_work: 0.3481 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 3524 Z= 0.308 Angle : 0.746 9.084 5015 Z= 0.392 Chirality : 0.047 0.170 571 Planarity : 0.007 0.049 450 Dihedral : 23.834 169.439 1055 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 9.48 % Favored : 89.66 % 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 aren not related in a simple way. whole: -1.38 (0.48), residues: 275 helix: -1.11 (0.49), residues: 99 sheet: -0.40 (1.04), residues: 28 loop : -0.79 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 271 TYR 0.011 0.002 TYR A 89 PHE 0.019 0.003 PHE A 350 TRP 0.022 0.003 TRP A 112 HIS 0.005 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 3524) covalent geometry : angle 0.74572 ( 5015) hydrogen bonds : bond 0.05796 ( 94) hydrogen bonds : angle 5.58490 ( 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 : 0.063 Fit side-chains REVERT: A 155 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6852 (ttp-170) REVERT: A 302 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8355 (mtpp) REVERT: A 330 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6946 (tm-30) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1221 time to fit residues: 5.1760 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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: 0.0870 chunk 6 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129027 restraints weight = 4984.264| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.35 r_work: 0.3512 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3524 Z= 0.140 Angle : 0.577 7.233 5015 Z= 0.303 Chirality : 0.039 0.130 571 Planarity : 0.005 0.040 450 Dihedral : 23.297 169.675 1055 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % 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 aren not related in a simple way. whole: -0.85 (0.49), residues: 275 helix: -0.38 (0.51), residues: 102 sheet: 0.02 (0.96), residues: 33 loop : -0.75 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.008 0.001 TYR A 201 PHE 0.010 0.001 PHE A 350 TRP 0.015 0.002 TRP A 318 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3524) covalent geometry : angle 0.57710 ( 5015) hydrogen bonds : bond 0.04108 ( 94) hydrogen bonds : angle 4.73867 ( 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: 5 poor density : 30 time to evaluate : 0.100 Fit side-chains REVERT: A 74 GLU cc_start: 0.7034 (mp0) cc_final: 0.6580 (mp0) REVERT: A 302 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8242 (mtpp) outliers start: 5 outliers final: 1 residues processed: 34 average time/residue: 0.1267 time to fit residues: 4.8905 Evaluate side-chains 29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128817 restraints weight = 4836.631| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.30 r_work: 0.3518 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2312 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= 0.143 Angle : 0.564 6.546 5015 Z= 0.295 Chirality : 0.038 0.138 571 Planarity : 0.005 0.037 450 Dihedral : 23.081 170.747 1051 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 15.52 % Favored : 81.03 % 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 aren not related in a simple way. whole: -0.69 (0.50), residues: 275 helix: -0.16 (0.51), residues: 104 sheet: -0.27 (0.92), residues: 33 loop : -0.63 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.016 0.002 PHE A 350 TRP 0.014 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3524) covalent geometry : angle 0.56384 ( 5015) hydrogen bonds : bond 0.03802 ( 94) hydrogen bonds : angle 4.50368 ( 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 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.101 Fit side-chains REVERT: A 74 GLU cc_start: 0.7028 (mp0) cc_final: 0.6582 (mp0) REVERT: A 111 ARG cc_start: 0.7165 (ptm-80) cc_final: 0.6677 (ptt90) REVERT: A 302 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8255 (mtpp) outliers start: 8 outliers final: 2 residues processed: 37 average time/residue: 0.1209 time to fit residues: 5.0475 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126361 restraints weight = 4852.439| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.32 r_work: 0.3490 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3524 Z= 0.172 Angle : 0.580 6.470 5015 Z= 0.303 Chirality : 0.040 0.146 571 Planarity : 0.006 0.038 450 Dihedral : 23.117 171.190 1051 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 18.10 % 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 aren not related in a simple way. whole: -0.65 (0.49), residues: 275 helix: -0.07 (0.51), residues: 104 sheet: -0.64 (0.96), residues: 28 loop : -0.56 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.008 0.001 TYR A 201 PHE 0.014 0.002 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3524) covalent geometry : angle 0.58029 ( 5015) hydrogen bonds : bond 0.04007 ( 94) hydrogen bonds : angle 4.48171 ( 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 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.110 Fit side-chains REVERT: A 74 GLU cc_start: 0.7105 (mp0) cc_final: 0.6595 (mp0) REVERT: A 111 ARG cc_start: 0.7186 (ptm-80) cc_final: 0.6700 (ptt90) REVERT: A 302 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8265 (mtpp) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.1198 time to fit residues: 5.0085 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 326 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: 0.3980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125698 restraints weight = 4838.539| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.30 r_work: 0.3487 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3524 Z= 0.178 Angle : 0.588 6.686 5015 Z= 0.308 Chirality : 0.040 0.147 571 Planarity : 0.005 0.038 450 Dihedral : 23.150 171.296 1051 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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 aren not related in a simple way. whole: -0.59 (0.49), residues: 275 helix: 0.06 (0.51), residues: 104 sheet: -0.66 (0.95), residues: 28 loop : -0.57 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.008 0.001 TYR A 201 PHE 0.014 0.002 PHE A 350 TRP 0.016 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3524) covalent geometry : angle 0.58818 ( 5015) hydrogen bonds : bond 0.04111 ( 94) hydrogen bonds : angle 4.57392 ( 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 46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.096 Fit side-chains REVERT: A 74 GLU cc_start: 0.7097 (mp0) cc_final: 0.6550 (mp0) REVERT: A 111 ARG cc_start: 0.7183 (ptm-80) cc_final: 0.6690 (ptt90) REVERT: A 302 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8261 (mtpp) REVERT: A 330 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6981 (tm-30) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1187 time to fit residues: 5.7067 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.057 ------------------------------------------------------------------------------- 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 318 TRP Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124113 restraints weight = 4903.198| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.31 r_work: 0.3456 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3524 Z= 0.238 Angle : 0.657 6.947 5015 Z= 0.341 Chirality : 0.044 0.199 571 Planarity : 0.006 0.040 450 Dihedral : 23.376 170.882 1051 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.74 % Allowed : 18.10 % Favored : 77.16 % 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 aren not related in a simple way. whole: -0.77 (0.48), residues: 275 helix: -0.04 (0.50), residues: 104 sheet: -0.91 (0.92), residues: 28 loop : -0.69 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 271 TYR 0.009 0.002 TYR A 89 PHE 0.018 0.002 PHE A 350 TRP 0.017 0.002 TRP A 112 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 3524) covalent geometry : angle 0.65701 ( 5015) hydrogen bonds : bond 0.04522 ( 94) hydrogen bonds : angle 4.83876 ( 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 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.074 Fit side-chains REVERT: A 74 GLU cc_start: 0.7154 (mp0) cc_final: 0.6551 (mp0) REVERT: A 111 ARG cc_start: 0.7207 (ptm-80) cc_final: 0.6736 (ptt90) REVERT: A 302 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8316 (mtpp) REVERT: A 330 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6968 (tm-30) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.1149 time to fit residues: 5.3398 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR 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 326 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: 0.5980 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125753 restraints weight = 4898.417| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.30 r_work: 0.3483 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3524 Z= 0.173 Angle : 0.594 6.740 5015 Z= 0.312 Chirality : 0.040 0.164 571 Planarity : 0.005 0.040 450 Dihedral : 23.274 170.899 1051 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.74 % Allowed : 18.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.49), residues: 275 helix: 0.26 (0.51), residues: 104 sheet: -0.63 (0.84), residues: 33 loop : -0.70 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.008 0.001 TYR A 201 PHE 0.013 0.002 PHE A 350 TRP 0.016 0.002 TRP A 112 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3524) covalent geometry : angle 0.59403 ( 5015) hydrogen bonds : bond 0.04208 ( 94) hydrogen bonds : angle 4.65244 ( 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 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.064 Fit side-chains REVERT: A 74 GLU cc_start: 0.7095 (mp0) cc_final: 0.6534 (mp0) REVERT: A 111 ARG cc_start: 0.7167 (ptm-80) cc_final: 0.6693 (ptt90) REVERT: A 302 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8268 (mtpp) REVERT: A 330 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6977 (tm-30) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.0911 time to fit residues: 4.5285 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 326 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: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126438 restraints weight = 4906.881| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.27 r_work: 0.3485 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3524 Z= 0.159 Angle : 0.594 7.859 5015 Z= 0.308 Chirality : 0.040 0.183 571 Planarity : 0.005 0.041 450 Dihedral : 23.254 170.788 1051 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.31 % Allowed : 18.10 % Favored : 77.59 % 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 aren not related in a simple way. whole: -0.50 (0.49), residues: 275 helix: 0.35 (0.51), residues: 104 sheet: -0.64 (0.85), residues: 33 loop : -0.71 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.012 0.002 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3524) covalent geometry : angle 0.59362 ( 5015) hydrogen bonds : bond 0.04188 ( 94) hydrogen bonds : angle 4.63637 ( 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 46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.069 Fit side-chains REVERT: A 74 GLU cc_start: 0.7053 (mp0) cc_final: 0.6507 (mp0) REVERT: A 111 ARG cc_start: 0.7163 (ptm-80) cc_final: 0.6700 (ptt90) REVERT: A 302 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8246 (mtpp) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.0888 time to fit residues: 4.3248 Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 279 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LEU 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128445 restraints weight = 4885.876| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.30 r_work: 0.3514 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3524 Z= 0.141 Angle : 0.583 7.092 5015 Z= 0.304 Chirality : 0.039 0.194 571 Planarity : 0.005 0.041 450 Dihedral : 23.157 171.093 1051 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.59 % Allowed : 19.40 % 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 aren not related in a simple way. whole: -0.35 (0.49), residues: 275 helix: 0.45 (0.52), residues: 104 sheet: -0.34 (0.89), residues: 33 loop : -0.66 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.010 0.002 PHE A 350 TRP 0.014 0.001 TRP A 112 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3524) covalent geometry : angle 0.58329 ( 5015) hydrogen bonds : bond 0.04015 ( 94) hydrogen bonds : angle 4.53470 ( 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 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.058 Fit side-chains REVERT: A 74 GLU cc_start: 0.7014 (mp0) cc_final: 0.6490 (mp0) REVERT: A 190 GLU cc_start: 0.6481 (mp0) cc_final: 0.6045 (mp0) REVERT: A 302 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8197 (mtpp) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.0840 time to fit residues: 3.8072 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 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 264 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 327 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 16 optimal weight: 0.0670 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127761 restraints weight = 4908.372| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.28 r_work: 0.3510 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3524 Z= 0.143 Angle : 0.584 8.136 5015 Z= 0.304 Chirality : 0.039 0.177 571 Planarity : 0.005 0.040 450 Dihedral : 23.093 171.342 1051 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.02 % Allowed : 18.97 % 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 aren not related in a simple way. whole: -0.24 (0.49), residues: 275 helix: 0.52 (0.52), residues: 104 sheet: -0.17 (0.91), residues: 33 loop : -0.61 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.017 0.002 PHE A 334 TRP 0.014 0.001 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3524) covalent geometry : angle 0.58416 ( 5015) hydrogen bonds : bond 0.04013 ( 94) hydrogen bonds : angle 4.47612 ( 247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 985.03 seconds wall clock time: 17 minutes 33.79 seconds (1053.79 seconds total)