Starting phenix.real_space_refine on Fri Sep 11 03:01:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfo_61434/09_2026/9jfo_61434.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 166 5.49 5 S 15 5.16 5 C 3762 2.51 5 N 1278 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3432 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 1 Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2807 Classifications: {'RNA': 131} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 66, 'rna3p_pyr': 52} Link IDs: {'rna2p': 13, 'rna3p': 117} Chain breaks: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.25 Number of scatterers: 6954 At special positions: 0 Unit cell: (105.002, 96.3425, 120.157, 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 15 16.00 P 166 15.00 O 1733 8.00 N 1278 7.00 C 3762 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: 0.50 Conformation dependent library (CDL) restraints added in 321.8 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 42.9% alpha, 8.1% beta 59 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.595A pdb=" N MET A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.654A pdb=" N ARG A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.782A pdb=" N LYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.610A pdb=" N ARG A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.560A pdb=" N ASP A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 373 removed outlier: 3.681A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 4.218A pdb=" N ASP A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 417 removed outlier: 4.050A pdb=" N PHE A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 147 removed outlier: 4.588A pdb=" N THR A 206 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 221 " --> pdb=" O MET A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.256A pdb=" N GLU A 248 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 377 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 140 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1282 1.33 - 1.45: 2555 1.45 - 1.57: 3252 1.57 - 1.69: 326 1.69 - 1.81: 26 Bond restraints: 7441 Sorted by residual: bond pdb=" O3' C F 172 " pdb=" P A F 173 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.20e-02 6.94e+03 1.52e+01 bond pdb=" C3' DT D 8 " pdb=" C2' DT D 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" O3' C F 20 " pdb=" P C F 21 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 8.16e+00 bond pdb=" O3' C F 16 " pdb=" P C F 17 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 7.81e+00 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.05e+00 ... (remaining 7436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10148 1.73 - 3.47: 649 3.47 - 5.20: 36 5.20 - 6.94: 5 6.94 - 8.67: 1 Bond angle restraints: 10839 Sorted by residual: angle pdb=" O5' G F 5 " pdb=" C5' G F 5 " pdb=" C4' G F 5 " ideal model delta sigma weight residual 109.40 113.05 -3.65 8.00e-01 1.56e+00 2.08e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" O2 C F 127 " pdb=" C2 C F 127 " pdb=" N3 C F 127 " ideal model delta sigma weight residual 121.90 118.77 3.13 7.00e-01 2.04e+00 2.00e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT C 12 " pdb=" C4 DT C 12 " pdb=" O4 DT C 12 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 10834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 4024 35.29 - 70.58: 497 70.58 - 105.87: 54 105.87 - 141.17: 4 141.17 - 176.46: 1 Dihedral angle restraints: 4580 sinusoidal: 3315 harmonic: 1265 Sorted by residual: dihedral pdb=" O4' C F 88 " pdb=" C1' C F 88 " pdb=" N1 C F 88 " pdb=" C2 C F 88 " ideal model delta sinusoidal sigma weight residual 232.00 55.54 176.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' U F 23 " pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" O3' U F 23 " ideal model delta sinusoidal sigma weight residual 147.00 118.68 28.32 1 8.00e+00 1.56e-02 1.80e+01 dihedral pdb=" C3' A F 175 " pdb=" C4' A F 175 " pdb=" O4' A F 175 " pdb=" C1' A F 175 " ideal model delta sinusoidal sigma weight residual 20.00 -6.65 26.65 1 8.00e+00 1.56e-02 1.59e+01 ... (remaining 4577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 896 0.042 - 0.084: 212 0.084 - 0.126: 91 0.126 - 0.168: 95 0.168 - 0.210: 9 Chirality restraints: 1303 Sorted by residual: chirality pdb=" C3' U F 136 " pdb=" C4' U F 136 " pdb=" O3' U F 136 " pdb=" C2' U F 136 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' A F 22 " pdb=" C4' A F 22 " pdb=" O3' A F 22 " pdb=" C2' A F 22 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" P G F 24 " pdb=" OP1 G F 24 " pdb=" OP2 G F 24 " pdb=" O5' G F 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.61 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1300 not shown) Planarity restraints: 781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 305 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ASN A 305 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A 305 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 306 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 127 " -0.019 2.00e-02 2.50e+03 1.28e-02 3.67e+00 pdb=" N1 C F 127 " 0.023 2.00e-02 2.50e+03 pdb=" C2 C F 127 " -0.016 2.00e-02 2.50e+03 pdb=" O2 C F 127 " 0.011 2.00e-02 2.50e+03 pdb=" N3 C F 127 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C F 127 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C F 127 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C F 127 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F 127 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 326 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO A 327 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.026 5.00e-02 4.00e+02 ... (remaining 778 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 423 2.70 - 3.25: 6648 3.25 - 3.80: 13058 3.80 - 4.35: 16145 4.35 - 4.90: 22882 Nonbonded interactions: 59156 Sorted by model distance: nonbonded pdb=" O2' A F 137 " pdb=" O4' A F 138 " model vdw 2.151 3.040 nonbonded pdb=" O2' A F 137 " pdb=" O5' A F 138 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR A 362 " pdb=" O2' U F 10 " model vdw 2.224 3.040 nonbonded pdb=" O2' U F 87 " pdb=" O2' U F 90 " model vdw 2.224 3.040 nonbonded pdb=" O2' C F 20 " pdb=" O2' A F 75 " model vdw 2.230 3.040 ... (remaining 59151 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 0.047 7441 Z= 0.331 Angle : 0.801 8.671 10839 Z= 0.632 Chirality : 0.057 0.210 1303 Planarity : 0.005 0.047 781 Dihedral : 24.180 176.458 3758 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.40), residues: 427 helix: 0.54 (0.42), residues: 160 sheet: -2.40 (0.70), residues: 49 loop : -1.60 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.015 0.002 TYR A 412 PHE 0.016 0.002 PHE A 273 TRP 0.025 0.003 TRP A 292 HIS 0.005 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.33 ( 7441) covalent geometry : angle 0.80080 / 0.63 (10839) hydrogen bonds : bond 0.13205 / 9.31 ( 289) hydrogen bonds : angle 5.54326 / 4.08 ( 682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.138 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1059 time to fit residues: 7.3158 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN A 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.236704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.190204 restraints weight = 9807.726| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 3.17 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 7441 Z= 0.317 Angle : 0.833 9.688 10839 Z= 0.435 Chirality : 0.051 0.421 1303 Planarity : 0.008 0.091 781 Dihedral : 25.602 173.114 2880 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.48 % Allowed : 9.92 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.38), residues: 427 helix: 0.00 (0.39), residues: 168 sheet: -2.79 (0.66), residues: 49 loop : -2.09 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.023 0.004 TYR A 412 PHE 0.027 0.004 PHE A 273 TRP 0.016 0.004 TRP A 292 HIS 0.011 0.003 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.32 ( 7441) covalent geometry : angle 0.83344 / 0.44 (10839) hydrogen bonds : bond 0.08597 / 5.55 ( 289) hydrogen bonds : angle 4.55020 / 3.37 ( 682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.5768 (ttm) cc_final: 0.5275 (ttm) REVERT: A 361 ASP cc_start: 0.4998 (OUTLIER) cc_final: 0.4788 (t0) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.1027 time to fit residues: 6.9491 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 361 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4861 r_free = 0.4861 target = 0.242262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.195644 restraints weight = 9811.285| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.80 r_work: 0.3980 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7441 Z= 0.141 Angle : 0.621 9.746 10839 Z= 0.335 Chirality : 0.040 0.300 1303 Planarity : 0.006 0.046 781 Dihedral : 25.588 174.732 2880 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.10 % Allowed : 13.77 % Favored : 85.12 % 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: -1.69 (0.39), residues: 427 helix: 0.12 (0.40), residues: 174 sheet: -2.38 (0.71), residues: 49 loop : -1.89 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 140 TYR 0.015 0.002 TYR A 72 PHE 0.017 0.002 PHE A 143 TRP 0.009 0.002 TRP A 235 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7441) covalent geometry : angle 0.62113 / 0.34 (10839) hydrogen bonds : bond 0.06255 / 4.12 ( 289) hydrogen bonds : angle 4.04918 / 2.98 ( 682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.6409 (ttm) cc_final: 0.6054 (ttm) REVERT: A 306 ILE cc_start: 0.8358 (pt) cc_final: 0.7281 (mt) REVERT: A 361 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5618 (t0) outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.0973 time to fit residues: 6.1084 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 361 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 40.0000 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4833 r_free = 0.4833 target = 0.238955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.192323 restraints weight = 9891.337| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.99 r_work: 0.3912 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7441 Z= 0.209 Angle : 0.678 9.238 10839 Z= 0.363 Chirality : 0.044 0.373 1303 Planarity : 0.006 0.046 781 Dihedral : 25.557 174.405 2880 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.20 % Allowed : 15.70 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.38), residues: 427 helix: 0.03 (0.39), residues: 174 sheet: -2.54 (0.67), residues: 49 loop : -2.07 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.017 0.003 TYR A 72 PHE 0.024 0.003 PHE A 143 TRP 0.018 0.003 TRP A 80 HIS 0.007 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 7441) covalent geometry : angle 0.67845 / 0.36 (10839) hydrogen bonds : bond 0.06971 / 4.51 ( 289) hydrogen bonds : angle 4.08574 / 3.03 ( 682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5946 (mmt) REVERT: A 361 ASP cc_start: 0.5977 (OUTLIER) cc_final: 0.5733 (t0) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.0725 time to fit residues: 4.8832 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 361 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 53 optimal weight: 50.0000 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4812 r_free = 0.4812 target = 0.236697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.187944 restraints weight = 9925.414| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.81 r_work: 0.3883 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 7441 Z= 0.254 Angle : 0.741 9.941 10839 Z= 0.393 Chirality : 0.047 0.395 1303 Planarity : 0.006 0.044 781 Dihedral : 25.529 173.177 2880 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.58 % Allowed : 17.08 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.38), residues: 427 helix: -0.14 (0.38), residues: 175 sheet: -2.83 (0.65), residues: 49 loop : -2.22 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.020 0.003 TYR A 72 PHE 0.032 0.003 PHE A 143 TRP 0.022 0.003 TRP A 80 HIS 0.008 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 ( 7441) covalent geometry : angle 0.74132 / 0.39 (10839) hydrogen bonds : bond 0.07684 / 4.92 ( 289) hydrogen bonds : angle 4.25537 / 3.20 ( 682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5916 (mm) REVERT: A 361 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.5821 (t0) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.0808 time to fit residues: 6.0265 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 286 ARG Chi-restraints excluded: chain A residue 361 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.0020 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.4326 ------------------------------------------------------------------------------- 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 = 0.4868 r_free = 0.4868 target = 0.243179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.196478 restraints weight = 9944.476| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.88 r_work: 0.3970 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7441 Z= 0.125 Angle : 0.597 9.362 10839 Z= 0.325 Chirality : 0.040 0.294 1303 Planarity : 0.005 0.047 781 Dihedral : 25.485 175.287 2880 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.20 % Allowed : 19.01 % Favored : 78.79 % 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: -1.63 (0.39), residues: 427 helix: 0.16 (0.39), residues: 176 sheet: -2.59 (0.65), residues: 54 loop : -1.74 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.015 0.002 TYR A 72 PHE 0.017 0.002 PHE A 37 TRP 0.024 0.002 TRP A 80 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 7441) covalent geometry : angle 0.59710 / 0.32 (10839) hydrogen bonds : bond 0.05738 / 3.71 ( 289) hydrogen bonds : angle 3.84795 / 2.86 ( 682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7526 (tmt170) REVERT: A 75 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5913 (mmt) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.1013 time to fit residues: 6.6576 Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 75 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 0.0270 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.4859 r_free = 0.4859 target = 0.242169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.195035 restraints weight = 9870.330| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.83 r_work: 0.3969 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7441 Z= 0.136 Angle : 0.607 11.866 10839 Z= 0.328 Chirality : 0.040 0.327 1303 Planarity : 0.005 0.053 781 Dihedral : 25.472 175.844 2880 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.38 % Allowed : 20.66 % Favored : 77.96 % 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: -1.68 (0.39), residues: 427 helix: 0.10 (0.39), residues: 180 sheet: -2.49 (0.63), residues: 54 loop : -1.84 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 286 TYR 0.013 0.002 TYR A 72 PHE 0.018 0.002 PHE A 143 TRP 0.019 0.002 TRP A 80 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 7441) covalent geometry : angle 0.60701 / 0.33 (10839) hydrogen bonds : bond 0.05792 / 3.74 ( 289) hydrogen bonds : angle 3.77918 / 2.81 ( 682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7566 (tmt170) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1074 time to fit residues: 6.5646 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 49 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 50.0000 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 50.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.241852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.196189 restraints weight = 9974.309| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.95 r_work: 0.3929 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7441 Z= 0.150 Angle : 0.611 11.367 10839 Z= 0.331 Chirality : 0.040 0.346 1303 Planarity : 0.005 0.055 781 Dihedral : 25.453 176.119 2880 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.10 % Allowed : 21.21 % Favored : 77.69 % 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: -1.68 (0.39), residues: 427 helix: 0.09 (0.39), residues: 180 sheet: -2.43 (0.64), residues: 54 loop : -1.85 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 286 TYR 0.013 0.002 TYR A 72 PHE 0.019 0.002 PHE A 143 TRP 0.020 0.002 TRP A 80 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 7441) covalent geometry : angle 0.61103 / 0.33 (10839) hydrogen bonds : bond 0.05839 / 3.75 ( 289) hydrogen bonds : angle 3.78718 / 2.81 ( 682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7636 (tmt170) REVERT: A 75 MET cc_start: 0.5843 (mmt) cc_final: 0.5446 (mmt) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.0931 time to fit residues: 5.7879 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 49 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.0670 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.244375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.198757 restraints weight = 9891.426| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 2.86 r_work: 0.3979 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7441 Z= 0.123 Angle : 0.587 11.341 10839 Z= 0.321 Chirality : 0.039 0.312 1303 Planarity : 0.005 0.046 781 Dihedral : 25.447 176.965 2880 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.10 % Allowed : 21.49 % Favored : 77.41 % 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: -1.54 (0.39), residues: 427 helix: 0.10 (0.39), residues: 181 sheet: -1.74 (0.72), residues: 49 loop : -1.89 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.013 0.001 TYR A 72 PHE 0.015 0.002 PHE A 143 TRP 0.021 0.003 TRP A 80 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 7441) covalent geometry : angle 0.58688 / 0.32 (10839) hydrogen bonds : bond 0.05335 / 3.45 ( 289) hydrogen bonds : angle 3.66934 / 2.70 ( 682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7499 (tmt170) REVERT: A 75 MET cc_start: 0.5673 (mmt) cc_final: 0.5331 (mmt) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.0927 time to fit residues: 5.8662 Evaluate side-chains 45 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 49 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.236232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.188428 restraints weight = 9964.500| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.86 r_work: 0.3870 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 7441 Z= 0.314 Angle : 0.798 10.626 10839 Z= 0.419 Chirality : 0.050 0.443 1303 Planarity : 0.007 0.055 781 Dihedral : 25.513 174.643 2880 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.10 % Allowed : 21.21 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.38), residues: 427 helix: -0.10 (0.39), residues: 169 sheet: -2.81 (0.60), residues: 54 loop : -2.00 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.021 0.004 TYR A 412 PHE 0.045 0.004 PHE A 143 TRP 0.023 0.004 TRP A 80 HIS 0.011 0.003 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.31 ( 7441) covalent geometry : angle 0.79846 / 0.42 (10839) hydrogen bonds : bond 0.08220 / 5.26 ( 289) hydrogen bonds : angle 4.24106 / 3.15 ( 682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7598 (tmt170) REVERT: A 29 GLN cc_start: 0.7245 (tt0) cc_final: 0.6916 (tt0) REVERT: A 75 MET cc_start: 0.6346 (mmt) cc_final: 0.6041 (mmt) outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.0883 time to fit residues: 5.3763 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 49 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.241971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.195098 restraints weight = 9716.766| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.85 r_work: 0.3970 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7441 Z= 0.132 Angle : 0.607 10.959 10839 Z= 0.331 Chirality : 0.040 0.315 1303 Planarity : 0.006 0.055 781 Dihedral : 25.473 175.909 2880 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.83 % Allowed : 20.94 % Favored : 78.24 % 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 (0.39), residues: 427 helix: 0.03 (0.39), residues: 176 sheet: -2.55 (0.63), residues: 54 loop : -1.84 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.015 0.002 TYR A 72 PHE 0.015 0.002 PHE A 143 TRP 0.024 0.003 TRP A 80 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7441) covalent geometry : angle 0.60684 / 0.33 (10839) hydrogen bonds : bond 0.05812 / 3.72 ( 289) hydrogen bonds : angle 3.84658 / 2.86 ( 682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.99 seconds wall clock time: 29 minutes 11.50 seconds (1751.50 seconds total)