Starting phenix.real_space_refine on Tue Aug 4 15:21:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2026/8wrv_37791.cif" } resolution = 3.28 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= 0.017 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 92 5.49 5 S 11 5.16 5 C 2479 2.51 5 N 813 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 4471 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2537 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 3 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 6, 'rna3p': 49} Time building chain proxies: 1.24, per 1000 atoms: 0.28 Number of scatterers: 4471 At special positions: 0 Unit cell: (60.72, 77.22, 114.84, 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 11 16.00 P 92 15.00 O 1076 8.00 N 813 7.00 C 2479 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: 0.41 Conformation dependent library (CDL) restraints added in 85.5 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 37.3% alpha, 20.9% beta 24 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.756A pdb=" N HIS A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.506A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.118A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.534A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.597A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.552A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.998A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.852A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 417 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 407 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 394 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.817A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.53 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: 1019 1.33 - 1.45: 1438 1.45 - 1.57: 2091 1.57 - 1.69: 181 1.69 - 1.81: 16 Bond restraints: 4745 Sorted by residual: bond pdb=" O3' A B -10 " pdb=" P G B -9 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" O3' C B 14 " pdb=" P C B 15 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" C3' DT C -12 " pdb=" C2' DT C -12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" O3' G B -36 " pdb=" P U B -35 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 1.375 1.400 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 4740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 6494 2.05 - 4.11: 310 4.11 - 6.16: 19 6.16 - 8.21: 2 8.21 - 10.27: 1 Bond angle restraints: 6826 Sorted by residual: angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" C1' G B -4 " pdb=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 126.50 131.91 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 6821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 2533 35.81 - 71.62: 278 71.62 - 107.43: 26 107.43 - 143.24: 2 143.24 - 179.05: 3 Dihedral angle restraints: 2842 sinusoidal: 1921 harmonic: 921 Sorted by residual: dihedral pdb=" O4' C B -6 " pdb=" C1' C B -6 " pdb=" N1 C B -6 " pdb=" C2 C B -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.44 149.56 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 200.00 53.31 146.69 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' U B -5 " pdb=" C1' U B -5 " pdb=" N1 U B -5 " pdb=" C2 U B -5 " ideal model delta sinusoidal sigma weight residual -128.00 51.05 -179.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 2839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 650 0.070 - 0.141: 134 0.141 - 0.211: 14 0.211 - 0.282: 0 0.282 - 0.352: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ARG A 41 " pdb=" N ARG A 41 " pdb=" C ARG A 41 " pdb=" CB ARG A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ARG A 416 " pdb=" N ARG A 416 " pdb=" C ARG A 416 " pdb=" CB ARG A 416 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 797 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 92 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 93 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C SER A 205 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 203 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.023 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1207 2.82 - 3.34: 3916 3.34 - 3.86: 8362 3.86 - 4.38: 9413 4.38 - 4.90: 13668 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" NH2 ARG A 47 " pdb=" OE2 GLU A 53 " model vdw 2.301 3.120 nonbonded pdb=" O2' C B -30 " pdb=" OP2 U B -29 " model vdw 2.351 3.040 nonbonded pdb=" O2 U B -27 " pdb=" N2 G B -12 " model vdw 2.358 2.496 nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.368 3.040 nonbonded pdb=" OP1 DA C 2 " pdb=" NZ LYS A 422 " model vdw 2.397 3.120 ... (remaining 36561 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: 4.640 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.620 Find NCS groups from input model: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.005 0.054 4745 Z= 0.405 Angle : 0.839 10.266 6826 Z= 0.660 Chirality : 0.059 0.352 800 Planarity : 0.005 0.051 547 Dihedral : 23.712 179.047 2244 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 0.74 % 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: -1.76 (0.47), residues: 308 helix: -0.50 (0.48), residues: 109 sheet: -1.31 (0.54), residues: 77 loop : -1.51 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.010 0.001 TYR A 22 PHE 0.021 0.001 PHE A 83 TRP 0.020 0.003 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.40 ( 4745) covalent geometry : angle 0.83926 / 0.66 ( 6826) hydrogen bonds : bond 0.16282 / 18.53 ( 165) hydrogen bonds : angle 7.07049 / 8.47 ( 412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.098 Fit side-chains REVERT: A 102 GLU cc_start: 0.7126 (pm20) cc_final: 0.6910 (pm20) REVERT: A 437 ILE cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.1142 time to fit residues: 8.1207 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146366 restraints weight = 6664.253| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.58 r_work: 0.3681 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4745 Z= 0.205 Angle : 0.647 8.758 6826 Z= 0.378 Chirality : 0.044 0.216 800 Planarity : 0.006 0.055 547 Dihedral : 25.596 179.644 1619 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % 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: -1.27 (0.47), residues: 308 helix: 0.25 (0.47), residues: 112 sheet: -1.14 (0.56), residues: 77 loop : -1.58 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 47 TYR 0.011 0.002 TYR A 22 PHE 0.018 0.002 PHE A 369 TRP 0.011 0.002 TRP A 229 HIS 0.007 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 ( 4745) covalent geometry : angle 0.64725 / 0.38 ( 6826) hydrogen bonds : bond 0.05605 / 6.26 ( 165) hydrogen bonds : angle 4.53277 / 5.37 ( 412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.067 Fit side-chains REVERT: A 96 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7917 (mmm-85) REVERT: A 102 GLU cc_start: 0.7609 (pm20) cc_final: 0.7374 (pm20) REVERT: A 438 ASP cc_start: 0.7239 (m-30) cc_final: 0.7039 (m-30) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.0702 time to fit residues: 4.1435 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 27 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.183375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146319 restraints weight = 6553.980| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.54 r_work: 0.3676 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4745 Z= 0.166 Angle : 0.577 7.668 6826 Z= 0.342 Chirality : 0.040 0.155 800 Planarity : 0.006 0.053 547 Dihedral : 25.581 179.342 1619 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.37 % Allowed : 11.48 % Favored : 88.15 % 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: -0.85 (0.48), residues: 308 helix: 0.74 (0.48), residues: 112 sheet: -0.86 (0.56), residues: 78 loop : -1.55 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.010 0.001 TYR A 22 PHE 0.015 0.002 PHE A 369 TRP 0.010 0.002 TRP A 229 HIS 0.004 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 ( 4745) covalent geometry : angle 0.57750 / 0.34 ( 6826) hydrogen bonds : bond 0.04968 / 5.67 ( 165) hydrogen bonds : angle 4.12623 / 4.82 ( 412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.109 Fit side-chains REVERT: A 56 VAL cc_start: 0.6890 (p) cc_final: 0.6611 (t) REVERT: A 102 GLU cc_start: 0.7632 (pm20) cc_final: 0.7368 (pm20) REVERT: A 438 ASP cc_start: 0.7384 (m-30) cc_final: 0.7146 (m-30) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.1009 time to fit residues: 5.8475 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.181036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143886 restraints weight = 6499.966| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.53 r_work: 0.3642 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4745 Z= 0.211 Angle : 0.628 8.996 6826 Z= 0.363 Chirality : 0.042 0.193 800 Planarity : 0.006 0.053 547 Dihedral : 25.686 178.372 1619 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.85 % Allowed : 12.22 % Favored : 85.93 % 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: -1.00 (0.48), residues: 308 helix: 0.57 (0.48), residues: 112 sheet: -0.85 (0.59), residues: 75 loop : -1.64 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.014 0.002 TYR A 22 PHE 0.017 0.002 PHE A 369 TRP 0.005 0.001 TRP A 229 HIS 0.005 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 ( 4745) covalent geometry : angle 0.62766 / 0.36 ( 6826) hydrogen bonds : bond 0.05221 / 5.66 ( 165) hydrogen bonds : angle 4.20558 / 4.99 ( 412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.113 Fit side-chains REVERT: A 102 GLU cc_start: 0.7672 (pm20) cc_final: 0.7410 (pm20) REVERT: A 437 ILE cc_start: 0.8544 (mm) cc_final: 0.8052 (mm) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1056 time to fit residues: 7.5091 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.183416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146129 restraints weight = 6627.346| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.55 r_work: 0.3663 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4745 Z= 0.147 Angle : 0.562 7.764 6826 Z= 0.332 Chirality : 0.039 0.160 800 Planarity : 0.005 0.050 547 Dihedral : 25.577 179.610 1619 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.85 % Allowed : 13.70 % Favored : 84.44 % 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: -0.70 (0.49), residues: 308 helix: 0.87 (0.48), residues: 113 sheet: -0.81 (0.59), residues: 75 loop : -1.47 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.011 0.001 TYR A 44 PHE 0.016 0.001 PHE A 169 TRP 0.009 0.002 TRP A 229 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 4745) covalent geometry : angle 0.56206 / 0.33 ( 6826) hydrogen bonds : bond 0.04524 / 5.14 ( 165) hydrogen bonds : angle 3.97705 / 4.61 ( 412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.110 Fit side-chains REVERT: A 20 ASP cc_start: 0.7090 (m-30) cc_final: 0.6677 (t0) REVERT: A 96 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7831 (mmt-90) REVERT: A 102 GLU cc_start: 0.7646 (pm20) cc_final: 0.7380 (pm20) REVERT: A 416 ARG cc_start: 0.8027 (tpt170) cc_final: 0.6835 (tpt170) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.1018 time to fit residues: 6.9327 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.182816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145429 restraints weight = 6687.700| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.57 r_work: 0.3652 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4745 Z= 0.167 Angle : 0.574 8.140 6826 Z= 0.335 Chirality : 0.039 0.160 800 Planarity : 0.006 0.056 547 Dihedral : 25.494 178.458 1619 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.11 % Allowed : 14.44 % Favored : 84.44 % 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: -0.60 (0.49), residues: 308 helix: 1.04 (0.50), residues: 112 sheet: -0.98 (0.58), residues: 77 loop : -1.30 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 47 TYR 0.010 0.002 TYR A 22 PHE 0.020 0.002 PHE A 31 TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 ( 4745) covalent geometry : angle 0.57438 / 0.34 ( 6826) hydrogen bonds : bond 0.04715 / 5.19 ( 165) hydrogen bonds : angle 3.95892 / 4.56 ( 412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.069 Fit side-chains REVERT: A 102 GLU cc_start: 0.7675 (pm20) cc_final: 0.7427 (pm20) REVERT: A 185 ASP cc_start: 0.7340 (t0) cc_final: 0.6950 (t0) REVERT: A 416 ARG cc_start: 0.7940 (tpt170) cc_final: 0.6964 (tpt170) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.0783 time to fit residues: 5.1658 Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.0040 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.3830 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.184000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146626 restraints weight = 6662.387| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.54 r_work: 0.3666 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4745 Z= 0.138 Angle : 0.543 8.687 6826 Z= 0.321 Chirality : 0.038 0.159 800 Planarity : 0.005 0.057 547 Dihedral : 25.387 178.847 1619 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.48 % Allowed : 16.30 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.49), residues: 308 helix: 1.23 (0.50), residues: 113 sheet: -0.83 (0.58), residues: 75 loop : -1.36 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 404 TYR 0.008 0.001 TYR A 44 PHE 0.008 0.001 PHE A 369 TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 ( 4745) covalent geometry : angle 0.54327 / 0.32 ( 6826) hydrogen bonds : bond 0.04359 / 4.92 ( 165) hydrogen bonds : angle 3.80897 / 4.36 ( 412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.066 Fit side-chains REVERT: A 102 GLU cc_start: 0.7674 (pm20) cc_final: 0.7422 (pm20) REVERT: A 185 ASP cc_start: 0.7288 (t0) cc_final: 0.6904 (t0) REVERT: A 416 ARG cc_start: 0.7907 (tpt170) cc_final: 0.6950 (tpt170) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0714 time to fit residues: 4.7190 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.184246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147002 restraints weight = 6629.087| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.56 r_work: 0.3671 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4745 Z= 0.135 Angle : 0.534 8.903 6826 Z= 0.315 Chirality : 0.037 0.158 800 Planarity : 0.005 0.057 547 Dihedral : 25.300 178.594 1619 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.11 % Allowed : 15.56 % Favored : 83.33 % 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: -0.34 (0.50), residues: 308 helix: 1.41 (0.50), residues: 112 sheet: -1.05 (0.56), residues: 77 loop : -1.16 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 404 TYR 0.007 0.001 TYR A 44 PHE 0.010 0.001 PHE A 31 TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 4745) covalent geometry : angle 0.53433 / 0.31 ( 6826) hydrogen bonds : bond 0.04315 / 4.82 ( 165) hydrogen bonds : angle 3.74917 / 4.22 ( 412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.069 Fit side-chains REVERT: A 102 GLU cc_start: 0.7658 (pm20) cc_final: 0.7434 (pm20) REVERT: A 185 ASP cc_start: 0.7329 (t0) cc_final: 0.6978 (t0) REVERT: A 416 ARG cc_start: 0.7851 (tpt170) cc_final: 0.6939 (tpt170) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.0641 time to fit residues: 4.3304 Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.183107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145914 restraints weight = 6649.630| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.56 r_work: 0.3618 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.003 0.026 4745 Z= 0.169 Angle : 0.570 9.059 6826 Z= 0.331 Chirality : 0.039 0.155 800 Planarity : 0.006 0.059 547 Dihedral : 25.363 177.261 1619 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.48 % Allowed : 16.67 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.49), residues: 308 helix: 1.18 (0.49), residues: 113 sheet: -0.94 (0.58), residues: 75 loop : -1.35 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.011 0.001 TYR A 22 PHE 0.010 0.001 PHE A 369 TRP 0.005 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 ( 4745) covalent geometry : angle 0.57010 / 0.33 ( 6826) hydrogen bonds : bond 0.04690 / 5.16 ( 165) hydrogen bonds : angle 3.82987 / 4.37 ( 412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.106 Fit side-chains REVERT: A 102 GLU cc_start: 0.7602 (pm20) cc_final: 0.7392 (pm20) REVERT: A 167 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.3979 (mtt180) REVERT: A 185 ASP cc_start: 0.7299 (t0) cc_final: 0.6945 (t0) REVERT: A 190 MET cc_start: 0.7906 (tpt) cc_final: 0.7706 (tpp) REVERT: A 416 ARG cc_start: 0.7954 (tpt170) cc_final: 0.7116 (tpt170) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.1089 time to fit residues: 7.1538 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 167 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.181756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145780 restraints weight = 6599.657| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.52 r_work: 0.3641 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4745 Z= 0.156 Angle : 0.557 9.020 6826 Z= 0.325 Chirality : 0.038 0.153 800 Planarity : 0.005 0.059 547 Dihedral : 25.358 177.261 1619 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.48 % Allowed : 17.04 % Favored : 81.48 % 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 are not related in a simple way. whole: -0.48 (0.50), residues: 308 helix: 1.28 (0.50), residues: 113 sheet: -0.96 (0.58), residues: 76 loop : -1.39 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.010 0.001 TYR A 22 PHE 0.010 0.001 PHE A 31 TRP 0.006 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 4745) covalent geometry : angle 0.55650 / 0.33 ( 6826) hydrogen bonds : bond 0.04538 / 5.02 ( 165) hydrogen bonds : angle 3.80008 / 4.33 ( 412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.073 Fit side-chains REVERT: A 102 GLU cc_start: 0.7640 (pm20) cc_final: 0.7405 (pm20) REVERT: A 167 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3979 (mtt180) REVERT: A 185 ASP cc_start: 0.7159 (t0) cc_final: 0.6814 (t0) REVERT: A 416 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7053 (tpt170) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.0817 time to fit residues: 5.5018 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 167 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.182707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146755 restraints weight = 6643.992| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.53 r_work: 0.3656 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4745 Z= 0.135 Angle : 0.536 8.747 6826 Z= 0.313 Chirality : 0.037 0.152 800 Planarity : 0.005 0.059 547 Dihedral : 25.334 177.661 1619 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % 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: -0.36 (0.50), residues: 308 helix: 1.40 (0.49), residues: 113 sheet: -0.93 (0.57), residues: 75 loop : -1.31 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 404 TYR 0.008 0.001 TYR A 22 PHE 0.008 0.001 PHE A 31 TRP 0.008 0.001 TRP A 229 HIS 0.001 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 ( 4745) covalent geometry : angle 0.53561 / 0.31 ( 6826) hydrogen bonds : bond 0.04321 / 4.82 ( 165) hydrogen bonds : angle 3.72797 / 4.23 ( 412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1210.54 seconds wall clock time: 21 minutes 19.08 seconds (1279.08 seconds total)