Starting phenix.real_space_refine on Tue Aug 4 21:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2026/9c0j_45086.cif" } resolution = 3.17 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= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 167 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3809 2.51 5 N 1240 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "R" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3313 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 26, 'rna3p': 128} Chain breaks: 4 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.39, per 1000 atoms: 0.20 Number of scatterers: 7010 At special positions: 0 Unit cell: (131.716, 110.5, 79.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 13 16.00 P 167 15.00 Mg 1 11.99 O 1779 8.00 N 1240 7.00 C 3809 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: 0.58 Conformation dependent library (CDL) restraints added in 320.9 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 53.4% alpha, 13.6% beta 58 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.603A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.630A pdb=" N ILE A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 101 removed outlier: 4.132A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.731A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.728A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.772A pdb=" N ALA A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.865A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.937A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 74 removed outlier: 3.780A pdb=" N ARG A 70 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 49 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.645A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 314 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 181 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 1.32 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: 1.19 - 1.32: 816 1.32 - 1.44: 2984 1.44 - 1.56: 3337 1.56 - 1.68: 334 1.68 - 1.81: 22 Bond restraints: 7493 Sorted by residual: bond pdb=" C1' DT P 8 " pdb=" N1 DT P 8 " ideal model delta sigma weight residual 1.468 1.568 -0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 1.468 1.567 -0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" O3B TTP A 502 " pdb=" PG TTP A 502 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" N1 DT P 5 " pdb=" C2 DT P 5 " ideal model delta sigma weight residual 1.376 1.415 -0.039 8.00e-03 1.56e+04 2.42e+01 bond pdb=" N9 A R 201 " pdb=" C4 A R 201 " ideal model delta sigma weight residual 1.374 1.396 -0.022 6.00e-03 2.78e+04 1.29e+01 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9941 2.04 - 4.08: 823 4.08 - 6.13: 94 6.13 - 8.17: 28 8.17 - 10.21: 11 Bond angle restraints: 10897 Sorted by residual: angle pdb=" O4' DT P 5 " pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 108.00 114.48 -6.48 7.00e-01 2.04e+00 8.58e+01 angle pdb=" O5' U R 173 " pdb=" C5' U R 173 " pdb=" C4' U R 173 " ideal model delta sigma weight residual 109.40 115.38 -5.98 8.00e-01 1.56e+00 5.59e+01 angle pdb=" O4' U R 173 " pdb=" C1' U R 173 " pdb=" N1 U R 173 " ideal model delta sigma weight residual 108.50 113.22 -4.72 7.00e-01 2.04e+00 4.55e+01 angle pdb=" C1' U R 268 " pdb=" N1 U R 268 " pdb=" C2 U R 268 " ideal model delta sigma weight residual 117.70 125.53 -7.83 1.20e+00 6.94e-01 4.25e+01 angle pdb=" C1' C R 269 " pdb=" N1 C R 269 " pdb=" C2 C R 269 " ideal model delta sigma weight residual 118.80 125.87 -7.07 1.10e+00 8.26e-01 4.13e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 4097 26.53 - 53.07: 366 53.07 - 79.60: 231 79.60 - 106.14: 13 106.14 - 132.67: 3 Dihedral angle restraints: 4710 sinusoidal: 3447 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U R 134 " pdb=" C1' U R 134 " pdb=" N1 U R 134 " pdb=" C2 U R 134 " ideal model delta sinusoidal sigma weight residual -160.00 -67.13 -92.87 1 1.50e+01 4.44e-03 4.48e+01 dihedral pdb=" O4' A R 201 " pdb=" C1' A R 201 " pdb=" N9 A R 201 " pdb=" C4 A R 201 " ideal model delta sinusoidal sigma weight residual 68.00 149.95 -81.95 1 1.70e+01 3.46e-03 2.86e+01 dihedral pdb=" CA ASP A 312 " pdb=" C ASP A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 992 0.073 - 0.145: 291 0.145 - 0.218: 36 0.218 - 0.291: 4 0.291 - 0.363: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C3' A R 210 " pdb=" C4' A R 210 " pdb=" O3' A R 210 " pdb=" C2' A R 210 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' U R 173 " pdb=" O4' U R 173 " pdb=" C2' U R 173 " pdb=" N1 U R 173 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' U R 224 " pdb=" O4' U R 224 " pdb=" C2' U R 224 " pdb=" N1 U R 224 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1321 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " -0.226 9.50e-02 1.11e+02 1.02e-01 7.97e+00 pdb=" NE ARG A 254 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 302 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LYS A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 204 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ARG A 204 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 204 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 374 2.71 - 3.32: 6416 3.32 - 3.92: 15484 3.92 - 4.53: 20134 4.53 - 5.14: 27208 Nonbonded interactions: 69616 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O1B TTP A 502 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 269 " pdb="MG MG A 501 " model vdw 2.119 2.170 nonbonded pdb=" O LEU A 141 " pdb="MG MG A 501 " model vdw 2.307 2.170 nonbonded pdb=" O TYR A 381 " pdb=" OG SER A 385 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" OD2 ASP A 169 " model vdw 2.385 3.040 ... (remaining 69611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.030 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.140 7493 Z= 0.417 Angle : 1.173 10.208 10897 Z= 1.030 Chirality : 0.068 0.363 1324 Planarity : 0.009 0.102 771 Dihedral : 21.848 132.671 3896 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.80 % Allowed : 4.29 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.36), residues: 423 helix: -0.83 (0.29), residues: 209 sheet: 1.28 (0.67), residues: 55 loop : 0.07 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 254 TYR 0.021 0.003 TYR A 89 PHE 0.021 0.003 PHE A 212 TRP 0.013 0.002 TRP A 8 HIS 0.006 0.002 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.42 ( 7493) covalent geometry : angle 1.17321 / 1.03 (10897) hydrogen bonds : bond 0.15167 / 10.36 ( 321) hydrogen bonds : angle 5.62385 / 3.92 ( 752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.122 Fit side-chains REVERT: A 198 ASN cc_start: 0.8565 (t0) cc_final: 0.8306 (t0) REVERT: A 205 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: A 246 MET cc_start: 0.8827 (mmm) cc_final: 0.8616 (mmt) REVERT: A 259 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 319 MET cc_start: 0.8333 (mtm) cc_final: 0.7991 (mtp) REVERT: A 329 ASP cc_start: 0.8330 (p0) cc_final: 0.8073 (p0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1292 time to fit residues: 9.1202 Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.166864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.116051 restraints weight = 7018.521| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 0.73 r_work: 0.2837 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7493 Z= 0.143 Angle : 0.580 6.503 10897 Z= 0.354 Chirality : 0.041 0.297 1324 Planarity : 0.005 0.036 771 Dihedral : 22.686 130.845 3014 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 4.83 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.39), residues: 423 helix: 0.63 (0.34), residues: 212 sheet: 1.41 (0.70), residues: 53 loop : 0.20 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 254 TYR 0.015 0.002 TYR A 245 PHE 0.011 0.002 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 7493) covalent geometry : angle 0.57990 / 0.35 (10897) hydrogen bonds : bond 0.07343 / 4.56 ( 321) hydrogen bonds : angle 3.89909 / 2.72 ( 752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.123 Fit side-chains REVERT: A 198 ASN cc_start: 0.8626 (t0) cc_final: 0.8239 (t0) REVERT: A 205 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: A 259 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 319 MET cc_start: 0.8612 (mtm) cc_final: 0.8225 (mtp) REVERT: A 352 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.7883 (mtt90) REVERT: A 410 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8032 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1491 time to fit residues: 8.2096 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 10.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.116198 restraints weight = 7016.969| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 0.78 r_work: 0.2725 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7493 Z= 0.123 Angle : 0.505 6.221 10897 Z= 0.308 Chirality : 0.037 0.290 1324 Planarity : 0.004 0.033 771 Dihedral : 22.541 130.400 3013 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.61 % Allowed : 7.77 % Favored : 90.62 % 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: 1.37 (0.40), residues: 423 helix: 1.34 (0.35), residues: 214 sheet: 1.71 (0.67), residues: 53 loop : 0.14 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.012 0.001 TYR A 245 PHE 0.009 0.001 PHE A 52 TRP 0.010 0.001 TRP A 157 HIS 0.004 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 7493) covalent geometry : angle 0.50530 / 0.31 (10897) hydrogen bonds : bond 0.06220 / 3.74 ( 321) hydrogen bonds : angle 3.50591 / 2.47 ( 752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.178 Fit side-chains REVERT: A 198 ASN cc_start: 0.8679 (t0) cc_final: 0.8271 (t0) REVERT: A 205 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: A 259 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 346 ARG cc_start: 0.8567 (mpt180) cc_final: 0.8325 (mmt-90) REVERT: A 352 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8064 (mtt90) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1317 time to fit residues: 7.8177 Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.163551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.110625 restraints weight = 7112.886| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 0.72 r_work: 0.2720 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7493 Z= 0.177 Angle : 0.566 6.666 10897 Z= 0.329 Chirality : 0.041 0.305 1324 Planarity : 0.005 0.036 771 Dihedral : 22.486 132.102 3013 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.68 % Allowed : 7.51 % Favored : 89.81 % 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: 1.03 (0.40), residues: 423 helix: 1.34 (0.35), residues: 214 sheet: 0.92 (0.62), residues: 64 loop : -0.31 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 410 TYR 0.016 0.002 TYR A 245 PHE 0.010 0.002 PHE A 47 TRP 0.010 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 7493) covalent geometry : angle 0.56625 / 0.33 (10897) hydrogen bonds : bond 0.06871 / 4.18 ( 321) hydrogen bonds : angle 3.54913 / 2.52 ( 752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: A 352 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.7954 (mtt90) outliers start: 10 outliers final: 9 residues processed: 51 average time/residue: 0.1405 time to fit residues: 8.8104 Evaluate side-chains 54 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.161544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.110754 restraints weight = 7061.066| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 0.73 r_work: 0.2698 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7493 Z= 0.216 Angle : 0.611 7.807 10897 Z= 0.348 Chirality : 0.043 0.303 1324 Planarity : 0.005 0.038 771 Dihedral : 22.486 134.600 3013 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.22 % Allowed : 8.31 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.39), residues: 423 helix: 1.07 (0.35), residues: 213 sheet: 0.78 (0.62), residues: 63 loop : -0.63 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 123 TYR 0.017 0.002 TYR A 245 PHE 0.010 0.002 PHE A 41 TRP 0.012 0.002 TRP A 157 HIS 0.005 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 ( 7493) covalent geometry : angle 0.61064 / 0.35 (10897) hydrogen bonds : bond 0.07361 / 4.50 ( 321) hydrogen bonds : angle 3.65311 / 2.59 ( 752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.168 Fit side-chains REVERT: A 119 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: A 352 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7924 (mtt90) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.1116 time to fit residues: 7.0644 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.167445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.114262 restraints weight = 7085.964| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 0.78 r_work: 0.2718 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7493 Z= 0.116 Angle : 0.496 5.715 10897 Z= 0.301 Chirality : 0.036 0.290 1324 Planarity : 0.004 0.036 771 Dihedral : 22.389 133.551 3013 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.61 % Allowed : 11.26 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.40), residues: 423 helix: 1.56 (0.36), residues: 212 sheet: 1.00 (0.63), residues: 64 loop : -0.57 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 306 TYR 0.012 0.001 TYR A 245 PHE 0.007 0.001 PHE A 52 TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 ( 7493) covalent geometry : angle 0.49568 / 0.30 (10897) hydrogen bonds : bond 0.06258 / 3.75 ( 321) hydrogen bonds : angle 3.47641 / 2.48 ( 752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.109 Fit side-chains REVERT: A 119 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 352 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8009 (mtt180) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.1164 time to fit residues: 6.5508 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.164528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.113208 restraints weight = 7077.772| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 0.74 r_work: 0.2701 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7493 Z= 0.211 Angle : 0.587 6.969 10897 Z= 0.333 Chirality : 0.041 0.300 1324 Planarity : 0.005 0.039 771 Dihedral : 22.405 134.538 3013 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.95 % Allowed : 9.92 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.40), residues: 423 helix: 1.30 (0.35), residues: 213 sheet: 0.82 (0.63), residues: 63 loop : -0.67 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 306 TYR 0.015 0.002 TYR A 245 PHE 0.011 0.002 PHE A 328 TRP 0.009 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 7493) covalent geometry : angle 0.58653 / 0.33 (10897) hydrogen bonds : bond 0.07092 / 4.31 ( 321) hydrogen bonds : angle 3.58562 / 2.55 ( 752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.108 Fit side-chains REVERT: A 119 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 352 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.7934 (mtt90) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.1181 time to fit residues: 7.1206 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 43 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.167262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.115911 restraints weight = 7083.411| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 0.76 r_work: 0.2736 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7493 Z= 0.111 Angle : 0.495 5.394 10897 Z= 0.300 Chirality : 0.036 0.298 1324 Planarity : 0.004 0.040 771 Dihedral : 22.395 133.791 3013 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.88 % Allowed : 10.99 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.40), residues: 423 helix: 1.73 (0.36), residues: 211 sheet: 0.98 (0.64), residues: 63 loop : -0.67 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 254 TYR 0.012 0.001 TYR A 245 PHE 0.009 0.001 PHE A 47 TRP 0.003 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 7493) covalent geometry : angle 0.49524 / 0.30 (10897) hydrogen bonds : bond 0.06164 / 3.69 ( 321) hydrogen bonds : angle 3.44799 / 2.46 ( 752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.113 Fit side-chains REVERT: A 119 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 352 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8021 (mtt180) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1117 time to fit residues: 6.3021 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.170040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116879 restraints weight = 7026.429| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 0.78 r_work: 0.2763 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7493 Z= 0.104 Angle : 0.471 5.216 10897 Z= 0.287 Chirality : 0.035 0.279 1324 Planarity : 0.004 0.038 771 Dihedral : 22.335 132.866 3013 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 10.72 % Favored : 87.94 % 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 (0.41), residues: 423 helix: 1.93 (0.36), residues: 212 sheet: 1.43 (0.64), residues: 66 loop : -0.59 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.011 0.001 TYR A 86 PHE 0.010 0.001 PHE A 52 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.10 ( 7493) covalent geometry : angle 0.47054 / 0.29 (10897) hydrogen bonds : bond 0.05821 / 3.46 ( 321) hydrogen bonds : angle 3.38152 / 2.43 ( 752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.107 Fit side-chains REVERT: A 352 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8024 (mtt180) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1109 time to fit residues: 6.0614 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 50.0000 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.165638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112851 restraints weight = 7071.345| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 0.75 r_work: 0.2652 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7493 Z= 0.220 Angle : 0.590 6.836 10897 Z= 0.332 Chirality : 0.042 0.297 1324 Planarity : 0.005 0.041 771 Dihedral : 22.414 134.745 3013 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % 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: 0.91 (0.40), residues: 423 helix: 1.40 (0.36), residues: 213 sheet: 1.02 (0.63), residues: 64 loop : -0.75 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 123 TYR 0.014 0.002 TYR A 245 PHE 0.010 0.002 PHE A 47 TRP 0.008 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 ( 7493) covalent geometry : angle 0.58964 / 0.33 (10897) hydrogen bonds : bond 0.07099 / 4.31 ( 321) hydrogen bonds : angle 3.52801 / 2.51 ( 752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.191 Fit side-chains REVERT: A 352 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.7995 (mtt90) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1016 time to fit residues: 5.5900 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 50.0000 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.167638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.114875 restraints weight = 7009.935| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.76 r_work: 0.2708 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7493 Z= 0.123 Angle : 0.499 5.364 10897 Z= 0.299 Chirality : 0.036 0.294 1324 Planarity : 0.004 0.044 771 Dihedral : 22.399 134.120 3013 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.61 % Allowed : 10.72 % Favored : 87.67 % 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: 1.17 (0.40), residues: 423 helix: 1.70 (0.36), residues: 211 sheet: 1.13 (0.63), residues: 64 loop : -0.73 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 12 TYR 0.013 0.001 TYR A 245 PHE 0.012 0.001 PHE A 52 TRP 0.004 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7493) covalent geometry : angle 0.49909 / 0.30 (10897) hydrogen bonds : bond 0.06280 / 3.77 ( 321) hydrogen bonds : angle 3.41842 / 2.44 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.79 seconds wall clock time: 25 minutes 7.57 seconds (1507.57 seconds total)