Starting phenix.real_space_refine on Thu Jul 2 05:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfo_61434/07_2026/9jfo_61434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfo_61434/07_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_61434/07_2026/9jfo_61434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfo_61434/07_2026/9jfo_61434.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfo_61434/07_2026/9jfo_61434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfo_61434/07_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-dev-6108/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: 1.46, per 1000 atoms: 0.21 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: 0.55 Conformation dependent library (CDL) restraints added in 189.8 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: 0.88 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: 1.11 Time building geometry restraints manager: 0.69 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 1.50e-02 4.44e+03 9.72e+00 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=" 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 bond pdb=" C1' DC C 14 " pdb=" N1 DC C 14 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.87e+00 bond pdb=" O3' C F 20 " pdb=" P C F 21 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.50e-02 4.44e+03 5.22e+00 ... (remaining 7436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10470 1.73 - 3.47: 329 3.47 - 5.20: 34 5.20 - 6.94: 5 6.94 - 8.67: 1 Bond angle restraints: 10839 Sorted by residual: angle pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" O3' U F 23 " ideal model delta sigma weight residual 109.40 118.07 -8.67 1.50e+00 4.44e-01 3.34e+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 - 0.045: 1042 0.045 - 0.090: 193 0.090 - 0.134: 53 0.134 - 0.179: 6 0.179 - 0.224: 9 Chirality restraints: 1303 Sorted by residual: chirality pdb=" C2' A F 173 " pdb=" C3' A F 173 " pdb=" O2' A F 173 " pdb=" C1' A F 173 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.22 2.00e-01 2.50e+01 1.25e+00 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 ... (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: 0.960 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.710 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- 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= 0.314 Angle : 0.678 8.671 10839 Z= 0.537 Chirality : 0.042 0.224 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 0.00423 / 0.31 ( 7441) covalent geometry : angle 0.67833 / 0.54 (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 : 0.148 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1209 time to fit residues: 8.3180 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 : 0.122 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.4815 r_free = 0.4815 target = 0.236773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.188905 restraints weight = 9824.314| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.15 r_work: 0.3867 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 7441 Z= 0.320 Angle : 0.772 8.928 10839 Z= 0.421 Chirality : 0.046 0.306 1303 Planarity : 0.007 0.089 781 Dihedral : 25.658 173.384 2880 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.20 % Allowed : 10.47 % Favored : 87.33 % 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: -1.96 (0.38), residues: 427 helix: 0.03 (0.40), residues: 168 sheet: -2.76 (0.66), residues: 49 loop : -2.05 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.023 0.004 TYR A 412 PHE 0.027 0.004 PHE A 143 TRP 0.017 0.004 TRP A 292 HIS 0.010 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.32 ( 7441) covalent geometry : angle 0.77186 / 0.42 (10839) hydrogen bonds : bond 0.08477 / 5.46 ( 289) hydrogen bonds : angle 4.54679 / 3.36 ( 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: 8 poor density : 48 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.6741 (ttm) cc_final: 0.6379 (ttm) REVERT: A 132 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7278 (mtm-85) REVERT: A 306 ILE cc_start: 0.8888 (tt) cc_final: 0.8668 (pt) REVERT: A 361 ASP cc_start: 0.5932 (OUTLIER) cc_final: 0.5668 (t0) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.1245 time to fit residues: 8.2681 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 : 0.102 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4860 r_free = 0.4860 target = 0.242083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.198334 restraints weight = 9818.813| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 3.18 r_work: 0.3941 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7441 Z= 0.148 Angle : 0.600 9.780 10839 Z= 0.334 Chirality : 0.038 0.240 1303 Planarity : 0.006 0.045 781 Dihedral : 25.645 174.813 2880 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.38 % Allowed : 13.77 % Favored : 84.85 % 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: -1.70 (0.39), residues: 427 helix: 0.12 (0.40), residues: 174 sheet: -2.39 (0.70), residues: 49 loop : -1.92 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 307 TYR 0.016 0.002 TYR A 72 PHE 0.017 0.002 PHE A 143 TRP 0.010 0.002 TRP A 235 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 7441) covalent geometry : angle 0.60009 / 0.33 (10839) hydrogen bonds : bond 0.06108 / 4.02 ( 289) hydrogen bonds : angle 4.03494 / 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 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.6456 (ttm) cc_final: 0.6096 (ttm) REVERT: A 132 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7149 (mtm-85) REVERT: A 306 ILE cc_start: 0.8887 (tt) cc_final: 0.8095 (pt) REVERT: A 361 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5668 (t0) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.0922 time to fit residues: 5.8781 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 49 HIS 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: 1.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4837 r_free = 0.4837 target = 0.239587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.195438 restraints weight = 9901.040| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 3.18 r_work: 0.3902 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7441 Z= 0.202 Angle : 0.640 9.503 10839 Z= 0.354 Chirality : 0.041 0.275 1303 Planarity : 0.006 0.046 781 Dihedral : 25.591 174.700 2880 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.48 % Allowed : 16.53 % Favored : 80.99 % 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: -1.86 (0.38), residues: 427 helix: 0.05 (0.39), residues: 174 sheet: -2.48 (0.67), residues: 49 loop : -2.06 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.017 0.003 TYR A 72 PHE 0.023 0.003 PHE A 143 TRP 0.019 0.003 TRP A 80 HIS 0.007 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 7441) covalent geometry : angle 0.64042 / 0.35 (10839) hydrogen bonds : bond 0.06670 / 4.32 ( 289) hydrogen bonds : angle 4.03520 / 3.00 ( 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 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5942 (mmt) REVERT: A 132 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7167 (mtm-85) REVERT: A 361 ASP cc_start: 0.5958 (OUTLIER) cc_final: 0.5708 (t0) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.0846 time to fit residues: 5.6791 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 325 VAL 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: 2.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4822 r_free = 0.4822 target = 0.237437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190244 restraints weight = 9933.213| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.92 r_work: 0.3886 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7441 Z= 0.235 Angle : 0.679 9.640 10839 Z= 0.375 Chirality : 0.042 0.282 1303 Planarity : 0.006 0.046 781 Dihedral : 25.537 173.825 2880 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.31 % Allowed : 16.80 % Favored : 79.89 % 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: -2.10 (0.38), residues: 427 helix: -0.09 (0.39), residues: 175 sheet: -2.78 (0.61), residues: 55 loop : -2.18 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 140 TYR 0.020 0.003 TYR A 72 PHE 0.030 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 0.00517 / 0.23 ( 7441) covalent geometry : angle 0.67904 / 0.37 (10839) hydrogen bonds : bond 0.07203 / 4.60 ( 289) hydrogen bonds : angle 4.14758 / 3.11 ( 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 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.6041 (mmt) REVERT: A 132 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7203 (mtm-85) REVERT: A 163 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5184 (mpt90) REVERT: A 164 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5933 (mm) REVERT: A 306 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8165 (pt) REVERT: A 361 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5794 (t0) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.0814 time to fit residues: 5.6265 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 163 ARG Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 306 ILE 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: 5.9990 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4850 r_free = 0.4850 target = 0.241083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.196859 restraints weight = 9894.104| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.86 r_work: 0.3951 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7441 Z= 0.146 Angle : 0.596 9.507 10839 Z= 0.333 Chirality : 0.039 0.245 1303 Planarity : 0.005 0.045 781 Dihedral : 25.514 174.939 2880 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.75 % Allowed : 19.56 % 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: -1.79 (0.39), residues: 427 helix: 0.03 (0.39), residues: 175 sheet: -2.65 (0.65), residues: 54 loop : -1.85 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 307 TYR 0.016 0.002 TYR A 72 PHE 0.018 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 0.00300 / 0.15 ( 7441) covalent geometry : angle 0.59633 / 0.33 (10839) hydrogen bonds : bond 0.05918 / 3.80 ( 289) hydrogen bonds : angle 3.96342 / 2.94 ( 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 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7593 (tmt170) REVERT: A 75 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5862 (mmt) REVERT: A 132 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7198 (mtm-85) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 0.0920 time to fit residues: 6.0172 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4831 r_free = 0.4831 target = 0.238903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.190315 restraints weight = 9680.612| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.02 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7441 Z= 0.189 Angle : 0.623 11.690 10839 Z= 0.345 Chirality : 0.040 0.274 1303 Planarity : 0.005 0.045 781 Dihedral : 25.504 175.033 2880 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.75 % Allowed : 19.83 % 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: -1.85 (0.38), residues: 427 helix: 0.03 (0.39), residues: 174 sheet: -2.48 (0.62), residues: 56 loop : -1.98 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.017 0.002 TYR A 72 PHE 0.024 0.002 PHE A 143 TRP 0.019 0.003 TRP A 80 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 7441) covalent geometry : angle 0.62316 / 0.35 (10839) hydrogen bonds : bond 0.06383 / 4.10 ( 289) hydrogen bonds : angle 3.97288 / 2.95 ( 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 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7216 (tmt170) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.0782 time to fit residues: 5.1430 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 40.0000 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 40.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.4848 r_free = 0.4848 target = 0.240954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.195357 restraints weight = 9963.860| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.89 r_work: 0.3946 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7441 Z= 0.159 Angle : 0.599 11.325 10839 Z= 0.333 Chirality : 0.039 0.257 1303 Planarity : 0.005 0.046 781 Dihedral : 25.488 175.497 2880 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.48 % Allowed : 20.66 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.39), residues: 427 helix: 0.06 (0.39), residues: 174 sheet: -2.50 (0.65), residues: 54 loop : -1.81 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.017 0.002 TYR A 72 PHE 0.019 0.002 PHE A 143 TRP 0.021 0.002 TRP A 80 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 7441) covalent geometry : angle 0.59875 / 0.33 (10839) hydrogen bonds : bond 0.05939 / 3.82 ( 289) hydrogen bonds : angle 3.90660 / 2.89 ( 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 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7533 (tmt170) REVERT: A 75 MET cc_start: 0.6181 (mmt) cc_final: 0.5931 (mmt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.1002 time to fit residues: 6.4973 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 52 optimal weight: 40.0000 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.3520 ------------------------------------------------------------------------------- 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 = 0.4836 r_free = 0.4836 target = 0.239670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.191416 restraints weight = 9794.373| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.75 r_work: 0.3928 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7441 Z= 0.189 Angle : 0.621 10.969 10839 Z= 0.344 Chirality : 0.040 0.273 1303 Planarity : 0.006 0.045 781 Dihedral : 25.479 175.487 2880 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.48 % Allowed : 20.94 % Favored : 76.58 % 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: -1.77 (0.38), residues: 427 helix: 0.04 (0.39), residues: 174 sheet: -2.51 (0.65), residues: 54 loop : -1.87 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.017 0.002 TYR A 72 PHE 0.025 0.002 PHE A 143 TRP 0.022 0.003 TRP A 80 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 7441) covalent geometry : angle 0.62128 / 0.34 (10839) hydrogen bonds : bond 0.06314 / 4.05 ( 289) hydrogen bonds : angle 3.94744 / 2.92 ( 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 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7624 (tmt170) REVERT: A 75 MET cc_start: 0.6189 (mmt) cc_final: 0.5940 (mmt) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.0906 time to fit residues: 6.1648 Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 43 optimal weight: 20.0000 overall best weight: 3.2164 ------------------------------------------------------------------------------- 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 = 0.4788 r_free = 0.4788 target = 0.233988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185762 restraints weight = 9931.147| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.99 r_work: 0.3826 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 7441 Z= 0.369 Angle : 0.844 10.383 10839 Z= 0.457 Chirality : 0.050 0.342 1303 Planarity : 0.008 0.063 781 Dihedral : 25.607 172.968 2880 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 1.93 % Allowed : 20.94 % Favored : 77.13 % 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: -2.22 (0.37), residues: 427 helix: -0.28 (0.38), residues: 169 sheet: -2.61 (0.73), residues: 44 loop : -2.24 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 358 TYR 0.023 0.004 TYR A 412 PHE 0.043 0.005 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 0.00822 / 0.37 ( 7441) covalent geometry : angle 0.84410 / 0.46 (10839) hydrogen bonds : bond 0.09187 / 5.87 ( 289) hydrogen bonds : angle 4.60308 / 3.42 ( 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 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7652 (tmt170) REVERT: A 306 ILE cc_start: 0.8587 (tt) cc_final: 0.8143 (pt) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.0747 time to fit residues: 5.0474 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 : 0.163 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4844 r_free = 0.4844 target = 0.240561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.194063 restraints weight = 9852.650| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.82 r_work: 0.3936 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7441 Z= 0.149 Angle : 0.620 12.531 10839 Z= 0.346 Chirality : 0.039 0.239 1303 Planarity : 0.005 0.044 781 Dihedral : 25.514 174.468 2880 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.48 % Allowed : 20.66 % Favored : 76.86 % 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: -1.95 (0.38), residues: 427 helix: -0.10 (0.39), residues: 175 sheet: -2.65 (0.64), residues: 54 loop : -1.96 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 307 TYR 0.018 0.002 TYR A 72 PHE 0.016 0.002 PHE A 37 TRP 0.025 0.003 TRP A 80 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 7441) covalent geometry : angle 0.61958 / 0.35 (10839) hydrogen bonds : bond 0.06185 / 3.97 ( 289) hydrogen bonds : angle 4.14311 / 3.06 ( 682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.29 seconds wall clock time: 29 minutes 6.79 seconds (1746.79 seconds total)