Starting phenix.real_space_refine on Thu Jul 2 04:52:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v48_64770/07_2026/9v48_64770.map" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3028 atoms to isotropic. 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 40 5.49 5 S 28 5.16 5 C 2430 2.51 5 N 753 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 4153 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3310 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 405} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 6, 'rna3p': 9} Chain: "F" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 515 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 6, 'rna3p': 17} Time building chain proxies: 1.05, per 1000 atoms: 0.25 Number of scatterers: 4153 At special positions: 0 Unit cell: (77.76, 103.68, 67.2, 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 28 16.00 P 40 15.00 O 902 8.00 N 753 7.00 C 2430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 124.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 60.5% alpha, 3.8% beta 4 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'D' and resid 21 through 48 removed outlier: 4.347A pdb=" N ILE D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 55 Processing helix chain 'D' and resid 56 through 71 removed outlier: 4.051A pdb=" N SER D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 129 through 148 removed outlier: 4.321A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 removed outlier: 3.795A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.998A pdb=" N SER D 165 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 166 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 209 through 230 Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.965A pdb=" N GLU D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 300 through 305 removed outlier: 4.675A pdb=" N PHE D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 335 removed outlier: 3.526A pdb=" N LYS D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.843A pdb=" N ILE D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 Processing helix chain 'D' and resid 438 through 438 No H-bonds generated for 'chain 'D' and resid 438 through 438' Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.898A pdb=" N GLU D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.506A pdb=" N GLU D 469 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AA2, first strand: chain 'D' and resid 95 through 100 removed outlier: 3.544A pdb=" N LYS D 98 " --> pdb=" O MET D 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 314 through 316 removed outlier: 4.002A pdb=" N SER D 314 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER D 377 " --> pdb=" O SER D 314 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1075 1.33 - 1.45: 955 1.45 - 1.57: 2143 1.57 - 1.69: 78 1.69 - 1.81: 50 Bond restraints: 4301 Sorted by residual: bond pdb=" CA ARG D 195 " pdb=" C ARG D 195 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.24e-02 6.50e+03 8.19e+00 bond pdb=" CA ARG D 174 " pdb=" C ARG D 174 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.38e-02 5.25e+03 5.07e+00 bond pdb=" O3' A F 1 " pdb=" P G F 2 " ideal model delta sigma weight residual 1.607 1.575 0.032 1.50e-02 4.44e+03 4.46e+00 bond pdb=" O3' G E 240 " pdb=" P C E 241 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.29e+00 bond pdb=" C ARG D 195 " pdb=" N MET D 196 " ideal model delta sigma weight residual 1.335 1.309 0.026 1.30e-02 5.92e+03 4.13e+00 ... (remaining 4296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5355 1.35 - 2.71: 485 2.71 - 4.06: 86 4.06 - 5.41: 25 5.41 - 6.76: 16 Bond angle restraints: 5967 Sorted by residual: angle pdb=" N ARG D 355 " pdb=" CA ARG D 355 " pdb=" C ARG D 355 " ideal model delta sigma weight residual 111.75 118.07 -6.32 1.28e+00 6.10e-01 2.44e+01 angle pdb=" N LYS D 357 " pdb=" CA LYS D 357 " pdb=" C LYS D 357 " ideal model delta sigma weight residual 113.23 107.11 6.12 1.24e+00 6.50e-01 2.43e+01 angle pdb=" N GLY D 86 " pdb=" CA GLY D 86 " pdb=" C GLY D 86 " ideal model delta sigma weight residual 111.54 105.19 6.35 1.36e+00 5.41e-01 2.18e+01 angle pdb=" N ASN D 76 " pdb=" CA ASN D 76 " pdb=" C ASN D 76 " ideal model delta sigma weight residual 111.28 106.26 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" O3' U E 227 " pdb=" C3' U E 227 " pdb=" C2' U E 227 " ideal model delta sigma weight residual 109.50 115.65 -6.15 1.50e+00 4.44e-01 1.68e+01 ... (remaining 5962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 2477 35.68 - 71.36: 182 71.36 - 107.04: 17 107.04 - 142.72: 3 142.72 - 178.40: 8 Dihedral angle restraints: 2687 sinusoidal: 1484 harmonic: 1203 Sorted by residual: dihedral pdb=" O4' U F 21 " pdb=" C1' U F 21 " pdb=" N1 U F 21 " pdb=" C2 U F 21 " ideal model delta sinusoidal sigma weight residual 200.00 44.14 155.86 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" C5' C E 241 " pdb=" C4' C E 241 " pdb=" C3' C E 241 " pdb=" O3' C E 241 " ideal model delta sinusoidal sigma weight residual 82.00 144.35 -62.35 1 8.00e+00 1.56e-02 8.04e+01 dihedral pdb=" O4' C E 241 " pdb=" C4' C E 241 " pdb=" C3' C E 241 " pdb=" C2' C E 241 " ideal model delta sinusoidal sigma weight residual -35.00 26.62 -61.62 1 8.00e+00 1.56e-02 7.87e+01 ... (remaining 2684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 519 0.055 - 0.111: 123 0.111 - 0.166: 31 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 683 Sorted by residual: chirality pdb=" C3' U E 227 " pdb=" C4' U E 227 " pdb=" O3' U E 227 " pdb=" C2' U E 227 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA PHE D 458 " pdb=" N PHE D 458 " pdb=" C PHE D 458 " pdb=" CB PHE D 458 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C3' U F 20 " pdb=" C4' U F 20 " pdb=" O3' U F 20 " pdb=" C2' U F 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 680 not shown) Planarity restraints: 630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 353 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO D 354 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 356 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLY D 356 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY D 356 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS D 357 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 282 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO D 283 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " -0.028 5.00e-02 4.00e+02 ... (remaining 627 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 614 2.74 - 3.28: 4758 3.28 - 3.82: 7303 3.82 - 4.36: 8352 4.36 - 4.90: 12126 Nonbonded interactions: 33153 Sorted by model distance: nonbonded pdb=" O ARG D 55 " pdb=" N TYR D 313 " model vdw 2.196 3.120 nonbonded pdb=" N ILE D 57 " pdb=" O TYR D 313 " model vdw 2.198 3.120 nonbonded pdb=" O LEU D 315 " pdb=" NZ LYS D 325 " model vdw 2.199 3.120 nonbonded pdb=" ND2 ASN D 417 " pdb=" OE1 GLU D 454 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR D 52 " pdb=" OG SER D 376 " model vdw 2.211 3.040 ... (remaining 33148 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.840 Find NCS groups from input model: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.006 0.056 4301 Z= 0.335 Angle : 0.922 6.764 5967 Z= 0.610 Chirality : 0.055 0.277 683 Planarity : 0.005 0.060 630 Dihedral : 24.490 178.403 1913 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 34.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.11 % Favored : 88.65 % Rotamer: Outliers : 4.55 % Allowed : 9.94 % Favored : 85.51 % 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: -4.85 (0.32), residues: 414 helix: -2.69 (0.26), residues: 213 sheet: -3.86 (0.79), residues: 26 loop : -3.72 (0.40), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 416 TYR 0.027 0.003 TYR D 97 PHE 0.011 0.002 PHE D 464 TRP 0.017 0.003 TRP D 330 HIS 0.007 0.002 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.33 ( 4301) covalent geometry : angle 0.92189 / 0.61 ( 5967) hydrogen bonds : bond 0.16897 / 11.54 ( 174) hydrogen bonds : angle 7.04767 / 5.12 ( 476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 TYR cc_start: 0.6786 (m-80) cc_final: 0.6052 (m-80) REVERT: D 103 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6908 (tmtt) REVERT: D 137 MET cc_start: 0.8931 (mtm) cc_final: 0.8647 (mtm) REVERT: D 156 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8440 (mmm160) REVERT: D 168 GLN cc_start: 0.7476 (tt0) cc_final: 0.7078 (tt0) REVERT: D 208 ARG cc_start: 0.1510 (OUTLIER) cc_final: 0.0547 (ttt180) REVERT: D 222 MET cc_start: 0.7848 (mmm) cc_final: 0.7617 (mmm) REVERT: D 235 GLN cc_start: 0.9033 (mt0) cc_final: 0.8775 (mt0) REVERT: D 331 MET cc_start: 0.5327 (ttp) cc_final: 0.4405 (ttm) REVERT: D 446 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8857 (ttm110) REVERT: D 447 MET cc_start: 0.8037 (mtp) cc_final: 0.7348 (tpp) REVERT: D 448 MET cc_start: 0.8335 (tmm) cc_final: 0.7281 (tmm) REVERT: D 458 PHE cc_start: 0.8024 (p90) cc_final: 0.7273 (p90) outliers start: 16 outliers final: 4 residues processed: 97 average time/residue: 0.1242 time to fit residues: 13.8560 Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS D 124 ASN D 135 HIS ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131535 restraints weight = 11462.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.133937 restraints weight = 7725.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135738 restraints weight = 5579.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136968 restraints weight = 4185.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137723 restraints weight = 3309.711| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4301 Z= 0.198 Angle : 0.783 6.210 5967 Z= 0.445 Chirality : 0.048 0.193 683 Planarity : 0.006 0.050 630 Dihedral : 26.349 174.159 1084 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.28 % Allowed : 5.68 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.36), residues: 414 helix: -1.60 (0.30), residues: 218 sheet: -4.25 (0.70), residues: 28 loop : -3.27 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 459 TYR 0.024 0.003 TYR D 78 PHE 0.017 0.002 PHE D 39 TRP 0.022 0.004 TRP D 139 HIS 0.008 0.003 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 4301) covalent geometry : angle 0.78296 / 0.45 ( 5967) hydrogen bonds : bond 0.05412 / 3.78 ( 174) hydrogen bonds : angle 5.60647 / 4.22 ( 476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 136 MET cc_start: 0.7828 (mtp) cc_final: 0.7397 (mtp) REVERT: D 156 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8326 (mmm160) REVERT: D 168 GLN cc_start: 0.7271 (tt0) cc_final: 0.6675 (tt0) REVERT: D 188 THR cc_start: 0.9719 (p) cc_final: 0.9505 (t) REVERT: D 240 ASP cc_start: 0.7700 (m-30) cc_final: 0.7203 (m-30) REVERT: D 277 PRO cc_start: 0.7501 (Cg_endo) cc_final: 0.6976 (Cg_exo) REVERT: D 443 GLU cc_start: 0.8260 (tt0) cc_final: 0.8026 (tt0) REVERT: D 447 MET cc_start: 0.7693 (mtp) cc_final: 0.7280 (tpt) REVERT: D 448 MET cc_start: 0.8706 (tmm) cc_final: 0.8106 (tmm) REVERT: D 458 PHE cc_start: 0.7851 (p90) cc_final: 0.7121 (p90) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1019 time to fit residues: 10.0267 Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134948 restraints weight = 10846.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137751 restraints weight = 7017.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.139593 restraints weight = 4824.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140858 restraints weight = 3569.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.141576 restraints weight = 2776.617| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4301 Z= 0.172 Angle : 0.720 9.237 5967 Z= 0.404 Chirality : 0.045 0.187 683 Planarity : 0.006 0.071 630 Dihedral : 26.146 175.767 1084 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.28 % Allowed : 4.83 % Favored : 94.89 % 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: -2.87 (0.38), residues: 414 helix: -0.81 (0.33), residues: 219 sheet: -3.81 (0.81), residues: 26 loop : -3.06 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 75 TYR 0.021 0.003 TYR D 78 PHE 0.010 0.002 PHE D 39 TRP 0.015 0.003 TRP D 330 HIS 0.005 0.001 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 4301) covalent geometry : angle 0.72031 / 0.40 ( 5967) hydrogen bonds : bond 0.04487 / 3.15 ( 174) hydrogen bonds : angle 5.09102 / 3.87 ( 476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 136 MET cc_start: 0.7824 (mtp) cc_final: 0.7575 (mtp) REVERT: D 137 MET cc_start: 0.8817 (mtm) cc_final: 0.8318 (mtm) REVERT: D 156 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8390 (mmm160) REVERT: D 168 GLN cc_start: 0.7568 (tt0) cc_final: 0.6759 (tt0) REVERT: D 216 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8400 (mtt-85) REVERT: D 443 GLU cc_start: 0.8538 (tt0) cc_final: 0.8134 (tt0) REVERT: D 446 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8646 (mtt180) REVERT: D 447 MET cc_start: 0.7710 (mtp) cc_final: 0.6974 (tpt) REVERT: D 448 MET cc_start: 0.8686 (tmm) cc_final: 0.7767 (tmm) REVERT: D 458 PHE cc_start: 0.7926 (p90) cc_final: 0.7167 (p90) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0995 time to fit residues: 9.6833 Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS D 142 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133692 restraints weight = 11422.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136160 restraints weight = 7546.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137936 restraints weight = 5386.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.139118 restraints weight = 4017.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140057 restraints weight = 3179.811| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4301 Z= 0.150 Angle : 0.686 8.042 5967 Z= 0.381 Chirality : 0.042 0.186 683 Planarity : 0.005 0.054 630 Dihedral : 26.074 177.789 1084 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.28 % Allowed : 3.41 % Favored : 96.31 % 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 (0.39), residues: 414 helix: -0.23 (0.34), residues: 220 sheet: -3.55 (0.85), residues: 26 loop : -2.76 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 459 TYR 0.019 0.002 TYR D 219 PHE 0.027 0.002 PHE D 464 TRP 0.014 0.002 TRP D 330 HIS 0.005 0.002 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 4301) covalent geometry : angle 0.68641 / 0.38 ( 5967) hydrogen bonds : bond 0.04103 / 2.89 ( 174) hydrogen bonds : angle 4.73236 / 3.63 ( 476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.6969 (m-30) cc_final: 0.6301 (t70) REVERT: D 113 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8555 (mtmt) REVERT: D 136 MET cc_start: 0.7936 (mtp) cc_final: 0.7573 (mtm) REVERT: D 137 MET cc_start: 0.8635 (mtm) cc_final: 0.8260 (mtm) REVERT: D 147 THR cc_start: 0.8498 (p) cc_final: 0.8055 (t) REVERT: D 156 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8339 (mmm160) REVERT: D 189 MET cc_start: 0.8241 (tpt) cc_final: 0.7972 (tpt) REVERT: D 196 MET cc_start: 0.7625 (mmt) cc_final: 0.7386 (mmt) REVERT: D 222 MET cc_start: 0.7148 (mmm) cc_final: 0.6755 (mmm) REVERT: D 255 ASP cc_start: 0.8996 (m-30) cc_final: 0.8753 (m-30) REVERT: D 292 GLU cc_start: 0.8363 (pt0) cc_final: 0.8145 (pt0) REVERT: D 443 GLU cc_start: 0.8342 (tt0) cc_final: 0.8025 (tt0) REVERT: D 446 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8619 (mtt180) REVERT: D 448 MET cc_start: 0.8562 (tmm) cc_final: 0.7718 (tmm) REVERT: D 459 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6299 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0994 time to fit residues: 9.6436 Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134280 restraints weight = 11246.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136819 restraints weight = 7528.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.138736 restraints weight = 5423.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140074 restraints weight = 4044.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141114 restraints weight = 3172.784| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4301 Z= 0.142 Angle : 0.647 6.560 5967 Z= 0.360 Chirality : 0.042 0.184 683 Planarity : 0.005 0.054 630 Dihedral : 25.996 178.948 1084 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -2.09 (0.39), residues: 414 helix: -0.18 (0.33), residues: 220 sheet: -3.31 (0.88), residues: 26 loop : -2.72 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 459 TYR 0.025 0.002 TYR D 78 PHE 0.015 0.002 PHE D 464 TRP 0.014 0.002 TRP D 139 HIS 0.004 0.001 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 4301) covalent geometry : angle 0.64744 / 0.36 ( 5967) hydrogen bonds : bond 0.03995 / 2.82 ( 174) hydrogen bonds : angle 4.66386 / 3.58 ( 476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7000 (m-30) cc_final: 0.6365 (t70) REVERT: D 113 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8507 (mtmt) REVERT: D 137 MET cc_start: 0.8679 (mtm) cc_final: 0.8256 (mtm) REVERT: D 156 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8356 (mmm160) REVERT: D 189 MET cc_start: 0.8296 (tpt) cc_final: 0.8032 (tpt) REVERT: D 196 MET cc_start: 0.7649 (mmt) cc_final: 0.7345 (mmt) REVERT: D 210 GLU cc_start: 0.8077 (pp20) cc_final: 0.7820 (pm20) REVERT: D 292 GLU cc_start: 0.8301 (pt0) cc_final: 0.8027 (pt0) REVERT: D 448 MET cc_start: 0.8628 (tmm) cc_final: 0.7737 (tmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0963 time to fit residues: 9.5205 Evaluate side-chains 71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 34 ASN D 82 HIS D 142 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132616 restraints weight = 11038.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135087 restraints weight = 7277.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136809 restraints weight = 5174.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137889 restraints weight = 3882.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138803 restraints weight = 3120.372| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4301 Z= 0.154 Angle : 0.672 6.580 5967 Z= 0.373 Chirality : 0.043 0.184 683 Planarity : 0.005 0.056 630 Dihedral : 25.918 179.913 1084 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.28 % Allowed : 1.70 % Favored : 98.01 % 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 (0.40), residues: 414 helix: -0.03 (0.34), residues: 219 sheet: -3.16 (0.94), residues: 26 loop : -2.52 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 121 TYR 0.015 0.002 TYR D 97 PHE 0.007 0.001 PHE D 346 TRP 0.015 0.002 TRP D 104 HIS 0.012 0.003 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 4301) covalent geometry : angle 0.67161 / 0.37 ( 5967) hydrogen bonds : bond 0.03989 / 2.82 ( 174) hydrogen bonds : angle 4.60076 / 3.52 ( 476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7097 (m-30) cc_final: 0.6491 (t70) REVERT: D 113 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8582 (mtmt) REVERT: D 147 THR cc_start: 0.8576 (p) cc_final: 0.8110 (t) REVERT: D 156 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8420 (tpt90) REVERT: D 189 MET cc_start: 0.8130 (tpt) cc_final: 0.7814 (tpt) REVERT: D 292 GLU cc_start: 0.8292 (pt0) cc_final: 0.7965 (pt0) REVERT: D 440 MET cc_start: 0.8742 (mtm) cc_final: 0.7442 (mtm) REVERT: D 443 GLU cc_start: 0.8505 (tt0) cc_final: 0.8239 (tt0) REVERT: D 448 MET cc_start: 0.8537 (tmm) cc_final: 0.7664 (tmm) REVERT: D 458 PHE cc_start: 0.7911 (p90) cc_final: 0.7295 (p90) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1008 time to fit residues: 10.2208 Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 chunk 2 optimal weight: 0.3980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134124 restraints weight = 11083.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136776 restraints weight = 7445.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138540 restraints weight = 5306.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.139900 restraints weight = 4053.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140806 restraints weight = 3181.952| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4301 Z= 0.142 Angle : 0.667 8.325 5967 Z= 0.366 Chirality : 0.042 0.182 683 Planarity : 0.005 0.054 630 Dihedral : 25.861 179.452 1084 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -1.71 (0.39), residues: 414 helix: 0.11 (0.34), residues: 219 sheet: -3.04 (0.97), residues: 26 loop : -2.51 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 459 TYR 0.025 0.002 TYR D 78 PHE 0.009 0.001 PHE D 230 TRP 0.021 0.003 TRP D 330 HIS 0.011 0.002 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 4301) covalent geometry : angle 0.66691 / 0.37 ( 5967) hydrogen bonds : bond 0.04010 / 2.85 ( 174) hydrogen bonds : angle 4.51617 / 3.48 ( 476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7012 (m-30) cc_final: 0.6437 (t70) REVERT: D 113 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8495 (mtmt) REVERT: D 147 THR cc_start: 0.8585 (p) cc_final: 0.8187 (t) REVERT: D 211 ASN cc_start: 0.8861 (p0) cc_final: 0.8565 (p0) REVERT: D 292 GLU cc_start: 0.8340 (pt0) cc_final: 0.7974 (pt0) REVERT: D 441 ARG cc_start: 0.8288 (mmp80) cc_final: 0.7985 (mmp80) REVERT: D 443 GLU cc_start: 0.8571 (tt0) cc_final: 0.8096 (tt0) REVERT: D 448 MET cc_start: 0.8433 (tmm) cc_final: 0.7592 (tmm) REVERT: D 458 PHE cc_start: 0.7901 (p90) cc_final: 0.7411 (p90) REVERT: D 459 ARG cc_start: 0.6785 (mtt90) cc_final: 0.6115 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0890 time to fit residues: 8.8731 Evaluate side-chains 70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 25 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 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 = 0.4005 r_free = 0.4005 target = 0.146040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132801 restraints weight = 11490.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135255 restraints weight = 7859.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136938 restraints weight = 5771.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138058 restraints weight = 4493.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139071 restraints weight = 3686.030| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4301 Z= 0.154 Angle : 0.676 8.910 5967 Z= 0.370 Chirality : 0.043 0.183 683 Planarity : 0.005 0.056 630 Dihedral : 25.778 179.128 1084 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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 (0.40), residues: 414 helix: -0.01 (0.33), residues: 223 sheet: -3.06 (0.99), residues: 26 loop : -2.51 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 75 TYR 0.019 0.002 TYR D 97 PHE 0.015 0.001 PHE D 230 TRP 0.015 0.003 TRP D 139 HIS 0.011 0.002 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4301) covalent geometry : angle 0.67648 / 0.37 ( 5967) hydrogen bonds : bond 0.03938 / 2.80 ( 174) hydrogen bonds : angle 4.45224 / 3.43 ( 476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7140 (m-30) cc_final: 0.6805 (t70) REVERT: D 147 THR cc_start: 0.8561 (p) cc_final: 0.8105 (t) REVERT: D 189 MET cc_start: 0.8731 (mmm) cc_final: 0.8200 (mmm) REVERT: D 211 ASN cc_start: 0.8853 (p0) cc_final: 0.8585 (p0) REVERT: D 292 GLU cc_start: 0.8314 (pt0) cc_final: 0.7955 (pt0) REVERT: D 448 MET cc_start: 0.8539 (tmm) cc_final: 0.7903 (tmm) REVERT: D 458 PHE cc_start: 0.7878 (p90) cc_final: 0.7503 (p90) REVERT: D 459 ARG cc_start: 0.7052 (mtt90) cc_final: 0.6266 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0901 time to fit residues: 9.0896 Evaluate side-chains 71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 32 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.0170 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 235 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 = 0.4025 r_free = 0.4025 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134687 restraints weight = 11144.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137253 restraints weight = 7590.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.138987 restraints weight = 5550.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139974 restraints weight = 4315.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141182 restraints weight = 3629.610| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4301 Z= 0.138 Angle : 0.700 10.144 5967 Z= 0.375 Chirality : 0.042 0.181 683 Planarity : 0.005 0.056 630 Dihedral : 25.743 178.783 1084 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.40), residues: 414 helix: 0.11 (0.34), residues: 224 sheet: -2.78 (1.07), residues: 26 loop : -2.48 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 441 TYR 0.027 0.002 TYR D 78 PHE 0.018 0.001 PHE D 230 TRP 0.028 0.003 TRP D 139 HIS 0.004 0.001 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4301) covalent geometry : angle 0.69979 / 0.37 ( 5967) hydrogen bonds : bond 0.04073 / 2.81 ( 174) hydrogen bonds : angle 4.43764 / 3.43 ( 476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7106 (m-30) cc_final: 0.6624 (t70) REVERT: D 147 THR cc_start: 0.8600 (p) cc_final: 0.8180 (t) REVERT: D 189 MET cc_start: 0.9018 (mmm) cc_final: 0.8690 (mmm) REVERT: D 211 ASN cc_start: 0.8856 (p0) cc_final: 0.8619 (p0) REVERT: D 222 MET cc_start: 0.7832 (tpp) cc_final: 0.7334 (tpp) REVERT: D 292 GLU cc_start: 0.8305 (pt0) cc_final: 0.7857 (pt0) REVERT: D 448 MET cc_start: 0.8533 (tmm) cc_final: 0.7853 (tmm) REVERT: D 458 PHE cc_start: 0.7902 (p90) cc_final: 0.7511 (p90) REVERT: D 459 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6076 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0832 time to fit residues: 8.5602 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.0070 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 31 optimal weight: 0.3980 chunk 44 optimal weight: 7.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.148796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134831 restraints weight = 10665.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137729 restraints weight = 7044.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139771 restraints weight = 5021.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141150 restraints weight = 3771.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.142220 restraints weight = 2974.550| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4301 Z= 0.134 Angle : 0.664 6.687 5967 Z= 0.361 Chirality : 0.041 0.180 683 Planarity : 0.005 0.056 630 Dihedral : 25.702 178.722 1084 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.43 % 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: -1.51 (0.41), residues: 414 helix: 0.21 (0.34), residues: 224 sheet: -2.68 (1.10), residues: 26 loop : -2.44 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 441 TYR 0.013 0.002 TYR D 97 PHE 0.019 0.001 PHE D 230 TRP 0.020 0.003 TRP D 139 HIS 0.006 0.002 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4301) covalent geometry : angle 0.66403 / 0.36 ( 5967) hydrogen bonds : bond 0.03806 / 2.64 ( 174) hydrogen bonds : angle 4.32769 / 3.34 ( 476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ASP cc_start: 0.7092 (m-30) cc_final: 0.6669 (t70) REVERT: D 137 MET cc_start: 0.8670 (mtm) cc_final: 0.8248 (mtm) REVERT: D 147 THR cc_start: 0.8544 (p) cc_final: 0.8127 (t) REVERT: D 189 MET cc_start: 0.8856 (mmm) cc_final: 0.8524 (mmm) REVERT: D 211 ASN cc_start: 0.8750 (p0) cc_final: 0.8498 (p0) REVERT: D 222 MET cc_start: 0.7553 (tpp) cc_final: 0.7242 (tpp) REVERT: D 235 GLN cc_start: 0.7832 (pt0) cc_final: 0.7539 (tt0) REVERT: D 292 GLU cc_start: 0.8271 (pt0) cc_final: 0.7808 (pt0) REVERT: D 374 MET cc_start: 0.6551 (mmp) cc_final: 0.6268 (mmm) REVERT: D 448 MET cc_start: 0.8532 (tmm) cc_final: 0.7828 (tmm) REVERT: D 459 ARG cc_start: 0.6823 (mtt90) cc_final: 0.6157 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.0801 time to fit residues: 7.9417 Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133404 restraints weight = 11187.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135887 restraints weight = 7625.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.137684 restraints weight = 5590.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139019 restraints weight = 4316.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.139967 restraints weight = 3432.738| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4301 Z= 0.143 Angle : 0.664 6.599 5967 Z= 0.363 Chirality : 0.042 0.182 683 Planarity : 0.006 0.064 630 Dihedral : 25.610 177.850 1084 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -1.51 (0.41), residues: 414 helix: 0.18 (0.34), residues: 223 sheet: -2.74 (1.10), residues: 26 loop : -2.37 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 441 TYR 0.025 0.002 TYR D 78 PHE 0.019 0.001 PHE D 230 TRP 0.020 0.003 TRP D 139 HIS 0.006 0.002 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 4301) covalent geometry : angle 0.66420 / 0.36 ( 5967) hydrogen bonds : bond 0.03926 / 2.74 ( 174) hydrogen bonds : angle 4.33201 / 3.33 ( 476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.75 seconds wall clock time: 16 minutes 26.64 seconds (986.64 seconds total)