Starting phenix.real_space_refine on Tue Mar 3 16:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfo_61434/03_2026/9jfo_61434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfo_61434/03_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_61434/03_2026/9jfo_61434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfo_61434/03_2026/9jfo_61434.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfo_61434/03_2026/9jfo_61434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfo_61434/03_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-5986/lib/python3.9/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: 1.48, 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: 0.62 Conformation dependent library (CDL) restraints added in 105.1 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: 1.10 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: 1.24 Time building geometry restraints manager: 0.75 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=" 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 bond pdb=" O3' C F 16 " pdb=" P C F 17 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.50e-02 4.44e+03 5.00e+00 bond pdb=" C1' C F 17 " pdb=" N1 C F 17 " ideal model delta sigma weight residual 1.480 1.456 0.024 1.50e-02 4.44e+03 2.48e+00 bond pdb=" O5' A F 175 " pdb=" C5' A F 175 " ideal model delta sigma weight residual 1.420 1.443 -0.023 1.50e-02 4.44e+03 2.25e+00 ... (remaining 7436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10542 1.73 - 3.47: 258 3.47 - 5.20: 33 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=" O3' A F 22 " pdb=" C3' A F 22 " pdb=" C2' A F 22 " ideal model delta sigma weight residual 113.70 107.75 5.95 1.50e+00 4.44e-01 1.58e+01 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" CB GLU A 309 " ideal model delta sigma weight residual 110.39 116.04 -5.65 1.66e+00 3.63e-01 1.16e+01 angle pdb=" O3' C F 88 " pdb=" C3' C F 88 " pdb=" C2' C F 88 " ideal model delta sigma weight residual 109.50 114.52 -5.02 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C3' G F 77 " pdb=" O3' G F 77 " pdb=" P A F 78 " ideal model delta sigma weight residual 120.20 124.82 -4.62 1.50e+00 4.44e-01 9.50e+00 ... (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: 1074 0.045 - 0.090: 169 0.090 - 0.134: 47 0.134 - 0.179: 4 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: 1.060 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.220 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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= 0.190 Angle : 0.642 8.671 10839 Z= 0.352 Chirality : 0.040 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 covalent geometry : bond 0.00382 ( 7441) covalent geometry : angle 0.64200 (10839) hydrogen bonds : bond 0.13205 ( 289) hydrogen bonds : angle 5.54326 ( 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 : 0.164 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1262 time to fit residues: 8.5679 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 : 0.144 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.237438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190443 restraints weight = 9835.776| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 3.06 r_work: 0.3882 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 7441 Z= 0.292 Angle : 0.771 9.914 10839 Z= 0.394 Chirality : 0.042 0.277 1303 Planarity : 0.007 0.060 781 Dihedral : 25.630 170.201 2880 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.48 % Allowed : 10.47 % Favored : 87.05 % 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: -1.99 (0.38), residues: 427 helix: -0.12 (0.38), residues: 174 sheet: -2.56 (0.68), residues: 49 loop : -2.06 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 140 TYR 0.019 0.003 TYR A 72 PHE 0.026 0.003 PHE A 273 TRP 0.020 0.003 TRP A 292 HIS 0.009 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 7441) covalent geometry : angle 0.77057 (10839) hydrogen bonds : bond 0.06787 ( 289) hydrogen bonds : angle 4.27470 ( 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 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: A 306 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (pt) REVERT: A 361 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.5652 (t0) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.1132 time to fit residues: 7.2468 Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 306 ILE 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: 1.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.242632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.196509 restraints weight = 9828.399| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.82 r_work: 0.3977 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7441 Z= 0.147 Angle : 0.633 9.382 10839 Z= 0.325 Chirality : 0.037 0.233 1303 Planarity : 0.005 0.046 781 Dihedral : 25.539 171.236 2880 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.48 % Allowed : 14.33 % Favored : 83.20 % 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: -1.61 (0.39), residues: 427 helix: 0.17 (0.40), residues: 175 sheet: -2.19 (0.72), residues: 49 loop : -1.88 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.016 0.002 TYR A 72 PHE 0.015 0.002 PHE A 143 TRP 0.018 0.002 TRP A 80 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7441) covalent geometry : angle 0.63289 (10839) hydrogen bonds : bond 0.05020 ( 289) hydrogen bonds : angle 3.81617 ( 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 55 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.6095 (ttm) cc_final: 0.5883 (ttm) REVERT: A 132 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7151 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.1092 time to fit residues: 7.3298 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 : 0.139 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain A residue 49 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.235246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.187705 restraints weight = 9905.424| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.92 r_work: 0.3861 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 7441 Z= 0.315 Angle : 0.802 10.587 10839 Z= 0.409 Chirality : 0.044 0.273 1303 Planarity : 0.006 0.047 781 Dihedral : 25.504 165.539 2880 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.65 % Allowed : 17.36 % 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: -2.19 (0.38), residues: 427 helix: -0.13 (0.39), residues: 174 sheet: -2.78 (0.60), residues: 55 loop : -2.27 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 140 TYR 0.019 0.003 TYR A 72 PHE 0.024 0.004 PHE A 143 TRP 0.016 0.003 TRP A 80 HIS 0.009 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 7441) covalent geometry : angle 0.80167 (10839) hydrogen bonds : bond 0.07300 ( 289) hydrogen bonds : angle 4.25286 ( 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: 6 poor density : 46 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.6024 (mmt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1251 time to fit residues: 7.8032 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 : 0.196 ------------------------------------------------------------------------------- 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 286 ARG 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: 1.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.240590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.194919 restraints weight = 9939.146| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.87 r_work: 0.3947 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7441 Z= 0.158 Angle : 0.652 11.771 10839 Z= 0.334 Chirality : 0.037 0.242 1303 Planarity : 0.005 0.048 781 Dihedral : 25.470 166.928 2880 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.20 % Allowed : 17.63 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.39), residues: 427 helix: 0.12 (0.40), residues: 175 sheet: -2.55 (0.64), residues: 54 loop : -1.98 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 307 TYR 0.017 0.002 TYR A 72 PHE 0.018 0.002 PHE A 143 TRP 0.020 0.003 TRP A 80 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7441) covalent geometry : angle 0.65174 (10839) hydrogen bonds : bond 0.05341 ( 289) hydrogen bonds : angle 3.85801 ( 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: 8 poor density : 48 time to evaluate : 0.161 Fit side-chains REVERT: A 132 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7203 (mtm-85) REVERT: A 234 THR cc_start: 0.8508 (m) cc_final: 0.8250 (p) REVERT: A 306 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7988 (mm) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.0983 time to fit residues: 6.9142 Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 286 ARG Chi-restraints excluded: chain A residue 306 ILE 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: 0.8980 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4872 r_free = 0.4872 target = 0.243553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.197143 restraints weight = 9914.586| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.88 r_work: 0.4000 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7441 Z= 0.138 Angle : 0.616 10.235 10839 Z= 0.318 Chirality : 0.036 0.241 1303 Planarity : 0.005 0.047 781 Dihedral : 25.383 171.008 2880 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.03 % Allowed : 17.91 % Favored : 79.06 % 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: -1.55 (0.39), residues: 427 helix: 0.19 (0.39), residues: 181 sheet: -1.89 (0.71), residues: 49 loop : -1.97 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.012 0.002 TYR A 72 PHE 0.014 0.002 PHE A 143 TRP 0.017 0.002 TRP A 80 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7441) covalent geometry : angle 0.61600 (10839) hydrogen bonds : bond 0.04665 ( 289) hydrogen bonds : angle 3.63838 ( 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 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.145 Fit side-chains REVERT: A 22 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7569 (tmt170) REVERT: A 75 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5581 (mmt) REVERT: A 132 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7171 (mtm-85) REVERT: A 234 THR cc_start: 0.8521 (m) cc_final: 0.8232 (p) REVERT: A 363 TYR cc_start: 0.7184 (t80) cc_final: 0.6826 (t80) outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 0.0980 time to fit residues: 6.9679 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 : 0.198 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 286 ARG Chi-restraints excluded: chain A residue 412 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 20.0000 chunk 5 optimal weight: 0.0770 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.245748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.199878 restraints weight = 9913.648| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 2.46 r_work: 0.4055 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7441 Z= 0.128 Angle : 0.607 9.886 10839 Z= 0.315 Chirality : 0.035 0.239 1303 Planarity : 0.005 0.047 781 Dihedral : 25.289 174.182 2880 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.65 % Allowed : 20.11 % 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: -1.47 (0.39), residues: 427 helix: 0.27 (0.39), residues: 181 sheet: -1.84 (0.71), residues: 53 loop : -1.93 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.010 0.001 TYR A 72 PHE 0.017 0.002 PHE A 37 TRP 0.016 0.002 TRP A 80 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7441) covalent geometry : angle 0.60721 (10839) hydrogen bonds : bond 0.04399 ( 289) hydrogen bonds : angle 3.46520 ( 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: 6 poor density : 46 time to evaluate : 0.133 Fit side-chains REVERT: A 22 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7569 (tmt170) REVERT: A 75 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5351 (mmt) REVERT: A 132 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7128 (mtm-85) REVERT: A 306 ILE cc_start: 0.8048 (pt) cc_final: 0.7435 (mm) REVERT: A 363 TYR cc_start: 0.7225 (t80) cc_final: 0.6840 (t80) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.0801 time to fit residues: 5.4411 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 : 0.172 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 412 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.238978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.191444 restraints weight = 9773.967| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.99 r_work: 0.3915 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2464 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= 0.215 Angle : 0.699 11.574 10839 Z= 0.359 Chirality : 0.039 0.271 1303 Planarity : 0.006 0.046 781 Dihedral : 25.318 172.604 2880 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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: -1.75 (0.38), residues: 427 helix: 0.01 (0.38), residues: 181 sheet: -2.23 (0.67), residues: 54 loop : -1.96 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.018 0.002 TYR A 72 PHE 0.016 0.003 PHE A 143 TRP 0.040 0.004 TRP A 235 HIS 0.007 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 7441) covalent geometry : angle 0.69887 (10839) hydrogen bonds : bond 0.05879 ( 289) hydrogen bonds : angle 3.78369 ( 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 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7539 (tmt170) REVERT: A 29 GLN cc_start: 0.6853 (tt0) cc_final: 0.6464 (tt0) REVERT: A 75 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5698 (mmt) REVERT: A 132 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7241 (mtm-85) REVERT: A 170 ASP cc_start: 0.7007 (p0) cc_final: 0.6619 (p0) REVERT: A 306 ILE cc_start: 0.8120 (pt) cc_final: 0.7915 (mm) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.0964 time to fit residues: 6.7260 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 : 0.118 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 412 TYR 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: 2.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.243590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.197269 restraints weight = 9867.469| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 2.40 r_work: 0.4021 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2545 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= 0.140 Angle : 0.631 11.629 10839 Z= 0.324 Chirality : 0.036 0.243 1303 Planarity : 0.005 0.046 781 Dihedral : 25.291 173.523 2880 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.20 % Allowed : 20.94 % 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: -1.52 (0.39), residues: 427 helix: 0.21 (0.39), residues: 181 sheet: -2.01 (0.70), residues: 54 loop : -1.87 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.013 0.002 TYR A 72 PHE 0.013 0.002 PHE A 37 TRP 0.029 0.003 TRP A 235 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7441) covalent geometry : angle 0.63076 (10839) hydrogen bonds : bond 0.04795 ( 289) hydrogen bonds : angle 3.60944 ( 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 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5588 (mmt) REVERT: A 132 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7164 (mtm-85) REVERT: A 170 ASP cc_start: 0.6880 (p0) cc_final: 0.6582 (p0) REVERT: A 306 ILE cc_start: 0.8072 (pt) cc_final: 0.7831 (mm) REVERT: A 478 MET cc_start: 0.0902 (ppp) cc_final: 0.0599 (ppp) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.0693 time to fit residues: 4.7933 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 : 0.156 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 412 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.235818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188093 restraints weight = 9934.688| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.81 r_work: 0.3870 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 7441 Z= 0.305 Angle : 0.791 10.997 10839 Z= 0.406 Chirality : 0.043 0.270 1303 Planarity : 0.006 0.046 781 Dihedral : 25.434 169.030 2880 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.20 % Allowed : 20.94 % 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: -1.87 (0.38), residues: 427 helix: 0.15 (0.40), residues: 165 sheet: -2.56 (0.62), residues: 54 loop : -2.04 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.019 0.003 TYR A 72 PHE 0.027 0.004 PHE A 143 TRP 0.035 0.004 TRP A 235 HIS 0.009 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 7441) covalent geometry : angle 0.79055 (10839) hydrogen bonds : bond 0.07240 ( 289) hydrogen bonds : angle 4.15211 ( 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: 8 poor density : 42 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.6404 (p0) cc_final: 0.5820 (m-30) REVERT: A 75 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.6074 (mmt) REVERT: A 170 ASP cc_start: 0.7267 (p0) cc_final: 0.6939 (p0) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.0928 time to fit residues: 5.8911 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.242505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.196517 restraints weight = 9921.735| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.43 r_work: 0.3976 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2774 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= 0.145 Angle : 0.641 11.604 10839 Z= 0.331 Chirality : 0.036 0.245 1303 Planarity : 0.005 0.045 781 Dihedral : 25.339 171.318 2880 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.65 % Allowed : 21.49 % 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: -1.66 (0.39), residues: 427 helix: 0.09 (0.39), residues: 176 sheet: -2.16 (0.67), residues: 54 loop : -1.87 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.011 0.002 TYR A 72 PHE 0.013 0.002 PHE A 37 TRP 0.023 0.003 TRP A 235 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7441) covalent geometry : angle 0.64066 (10839) hydrogen bonds : bond 0.04941 ( 289) hydrogen bonds : angle 3.73849 ( 682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.25 seconds wall clock time: 31 minutes 20.37 seconds (1880.37 seconds total)