Starting phenix.real_space_refine on Thu Jul 2 10:06:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.map" model { file = "/net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liq_63120/07_2026/9liq_63120.cif" } resolution = 3.04 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= 0.025 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 Zn 1 6.06 5 P 194 5.49 5 Mg 3 5.21 5 S 27 5.16 5 C 4347 2.51 5 N 1520 2.21 5 O 2039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 8131 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3984 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 473} Chain: "B" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 4061 Classifications: {'RNA': 190} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 12, 'rna3p_pur': 87, 'rna3p_pyr': 74} Link IDs: {'rna2p': 29, 'rna3p': 160} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1878 SG CYS A 234 17.538 12.895 60.187 1.00104.52 S ATOM 1903 SG CYS A 237 14.698 11.437 58.143 1.00117.65 S ATOM 2131 SG CYS A 265 18.211 9.891 57.759 1.00 95.56 S Time building chain proxies: 1.90, per 1000 atoms: 0.23 Number of scatterers: 8131 At special positions: 0 Unit cell: (98.412, 110.088, 120.93, 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) Zn 1 29.99 S 27 16.00 P 194 15.00 Mg 3 11.99 O 2039 8.00 N 1520 7.00 C 4347 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: 0.64 Conformation dependent library (CDL) restraints added in 281.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 268 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 237 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 234 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 265 " Number of angles added : 3 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 32.5% alpha, 15.4% beta 57 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.801A pdb=" N ARG A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 3.985A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 163 through 182 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.749A pdb=" N ALA A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 294 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.794A pdb=" N HIS A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 removed outlier: 3.823A pdb=" N CYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.081A pdb=" N ALA A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 478 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.695A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR A 41 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.692A pdb=" N LYS A 188 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 192 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 72 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 77 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 369 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.508A pdb=" N HIS A 243 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 396 removed outlier: 3.982A pdb=" N ALA A 395 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 386 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 471 removed outlier: 6.925A pdb=" N VAL A 470 " --> pdb=" O ARG A 456 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1769 1.33 - 1.45: 2894 1.45 - 1.57: 3610 1.57 - 1.69: 386 1.69 - 1.81: 42 Bond restraints: 8701 Sorted by residual: bond pdb=" N1 U B 94 " pdb=" C2 U B 94 " ideal model delta sigma weight residual 1.381 1.401 -0.020 9.00e-03 1.23e+04 4.71e+00 bond pdb=" N3 C B 46 " pdb=" C4 C B 46 " ideal model delta sigma weight residual 1.335 1.321 0.014 7.00e-03 2.04e+04 4.21e+00 bond pdb=" N PHE A 152 " pdb=" CA PHE A 152 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.96e+00 bond pdb=" C1' DC C 4 " pdb=" N1 DC C 4 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.88e+00 bond pdb=" C2' DC C 4 " pdb=" C1' DC C 4 " ideal model delta sigma weight residual 1.518 1.538 -0.020 1.00e-02 1.00e+04 3.85e+00 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12273 1.82 - 3.65: 332 3.65 - 5.47: 54 5.47 - 7.30: 15 7.30 - 9.12: 8 Bond angle restraints: 12682 Sorted by residual: angle pdb=" N1 U B 94 " pdb=" C2 U B 94 " pdb=" O2 U B 94 " ideal model delta sigma weight residual 122.80 128.12 -5.32 7.00e-01 2.04e+00 5.77e+01 angle pdb=" O2 U B 94 " pdb=" C2 U B 94 " pdb=" N3 U B 94 " ideal model delta sigma weight residual 122.20 117.57 4.63 7.00e-01 2.04e+00 4.37e+01 angle pdb=" N1 C B 46 " pdb=" C2 C B 46 " pdb=" O2 C B 46 " ideal model delta sigma weight residual 118.90 122.79 -3.89 6.00e-01 2.78e+00 4.21e+01 angle pdb=" C1' U B 171 " pdb=" N1 U B 171 " pdb=" C2 U B 171 " ideal model delta sigma weight residual 117.70 125.45 -7.75 1.20e+00 6.94e-01 4.17e+01 angle pdb=" O2 C B 46 " pdb=" C2 C B 46 " pdb=" N3 C B 46 " ideal model delta sigma weight residual 121.90 117.48 4.42 7.00e-01 2.04e+00 3.99e+01 ... (remaining 12677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 4866 35.64 - 71.28: 542 71.28 - 106.93: 64 106.93 - 142.57: 2 142.57 - 178.21: 8 Dihedral angle restraints: 5482 sinusoidal: 4044 harmonic: 1438 Sorted by residual: dihedral pdb=" O4' C B 46 " pdb=" C1' C B 46 " pdb=" N1 C B 46 " pdb=" C2 C B 46 " ideal model delta sinusoidal sigma weight residual -160.00 -7.88 -152.12 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U B 190 " pdb=" C1' U B 190 " pdb=" N1 U B 190 " pdb=" C2 U B 190 " ideal model delta sinusoidal sigma weight residual 200.00 74.55 125.45 1 1.50e+01 4.44e-03 6.74e+01 dihedral pdb=" O4' U B 93 " pdb=" C1' U B 93 " pdb=" N1 U B 93 " pdb=" C2 U B 93 " ideal model delta sinusoidal sigma weight residual -128.00 50.21 -178.21 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1290 0.047 - 0.095: 195 0.095 - 0.142: 44 0.142 - 0.189: 11 0.189 - 0.236: 5 Chirality restraints: 1545 Sorted by residual: chirality pdb=" C3' A B 83 " pdb=" C4' A B 83 " pdb=" O3' A B 83 " pdb=" C2' A B 83 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' U B 29 " pdb=" C4' U B 29 " pdb=" O3' U B 29 " pdb=" C2' U B 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1542 not shown) Planarity restraints: 901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 106 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C ARG A 106 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG A 106 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 107 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO A 164 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 210 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" CD GLN A 210 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 210 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 210 " -0.014 2.00e-02 2.50e+03 ... (remaining 898 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 469 2.70 - 3.25: 7227 3.25 - 3.80: 15132 3.80 - 4.35: 19528 4.35 - 4.90: 27369 Nonbonded interactions: 69725 Sorted by model distance: nonbonded pdb=" ND1 HIS A 245 " pdb="MG MG A 603 " model vdw 2.155 2.250 nonbonded pdb=" O6 G B 134 " pdb=" O2 U B 142 " model vdw 2.366 2.432 nonbonded pdb=" O4 U B 62 " pdb=" O6 G B 117 " model vdw 2.374 2.432 nonbonded pdb=" O2 U B 62 " pdb=" N2 G B 117 " model vdw 2.473 2.496 nonbonded pdb=" O5' G B 30 " pdb=" O4' G B 30 " model vdw 2.502 2.432 ... (remaining 69720 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8705 Z= 0.280 Angle : 0.767 9.125 12685 Z= 0.585 Chirality : 0.041 0.236 1545 Planarity : 0.006 0.062 901 Dihedral : 23.998 178.209 4558 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.13 % Favored : 90.26 % Rotamer: Outliers : 3.73 % Allowed : 30.54 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.18 (0.38), residues: 493 helix: -0.04 (0.42), residues: 157 sheet: -2.03 (0.51), residues: 95 loop : -2.15 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 261 TYR 0.021 0.002 TYR A 327 PHE 0.022 0.002 PHE A 329 TRP 0.012 0.001 TRP A 209 HIS 0.011 0.002 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.28 ( 8701) covalent geometry : angle 0.76634 / 0.58 (12682) hydrogen bonds : bond 0.14113 / 9.71 ( 300) hydrogen bonds : angle 6.56733 / 4.43 ( 685) metal coordination : bond 0.01670 / 0.84 ( 4) metal coordination : angle 2.09811 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.260 Fit side-chains REVERT: A 53 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6634 (mp10) REVERT: A 65 ASN cc_start: 0.7895 (m-40) cc_final: 0.7678 (m-40) REVERT: A 278 TRP cc_start: 0.8269 (m100) cc_final: 0.7752 (m100) REVERT: A 340 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6562 (t80) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.1311 time to fit residues: 12.6110 Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS A 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109605 restraints weight = 11148.353| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.56 r_work: 0.3221 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 8705 Z= 0.470 Angle : 0.896 9.485 12685 Z= 0.495 Chirality : 0.055 0.327 1545 Planarity : 0.009 0.090 901 Dihedral : 24.182 173.987 3556 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 1.01 % Allowed : 10.75 % Favored : 88.24 % Rotamer: Outliers : 7.69 % Allowed : 26.57 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.59 (0.37), residues: 493 helix: -0.57 (0.40), residues: 154 sheet: -1.85 (0.51), residues: 95 loop : -2.44 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 261 TYR 0.015 0.003 TYR A 327 PHE 0.028 0.003 PHE A 329 TRP 0.005 0.002 TRP A 161 HIS 0.010 0.002 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.47 ( 8701) covalent geometry : angle 0.89236 / 0.49 (12682) hydrogen bonds : bond 0.08660 / 5.75 ( 300) hydrogen bonds : angle 5.38704 / 3.69 ( 685) metal coordination : bond 0.01154 / 0.57 ( 4) metal coordination : angle 5.65652 / 3.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.193 Fit side-chains REVERT: A 37 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5830 (ptt-90) REVERT: A 143 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7872 (mttt) REVERT: A 250 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7647 (ptp-170) REVERT: A 256 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: A 276 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7688 (mptt) outliers start: 33 outliers final: 22 residues processed: 88 average time/residue: 0.1133 time to fit residues: 12.8381 Evaluate side-chains 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS A 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115943 restraints weight = 10944.480| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.43 r_work: 0.3317 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8705 Z= 0.161 Angle : 0.628 8.831 12685 Z= 0.360 Chirality : 0.040 0.269 1545 Planarity : 0.005 0.064 901 Dihedral : 24.080 178.831 3549 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.72 % Favored : 90.67 % Rotamer: Outliers : 5.83 % Allowed : 28.21 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.18 (0.38), residues: 493 helix: -0.09 (0.40), residues: 158 sheet: -1.83 (0.50), residues: 95 loop : -2.22 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 456 TYR 0.013 0.002 TYR A 494 PHE 0.016 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 8701) covalent geometry : angle 0.62752 / 0.36 (12682) hydrogen bonds : bond 0.06266 / 4.11 ( 300) hydrogen bonds : angle 4.87428 / 3.34 ( 685) metal coordination : bond 0.01038 / 0.52 ( 4) metal coordination : angle 1.72744 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8029 (m-40) cc_final: 0.7828 (m-40) REVERT: A 73 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 256 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: A 276 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7672 (mptt) outliers start: 25 outliers final: 16 residues processed: 83 average time/residue: 0.0866 time to fit residues: 9.4061 Evaluate side-chains 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 333 HIS ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114768 restraints weight = 11131.810| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.43 r_work: 0.3296 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8705 Z= 0.202 Angle : 0.634 8.508 12685 Z= 0.361 Chirality : 0.041 0.248 1545 Planarity : 0.005 0.065 901 Dihedral : 24.024 178.543 3547 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.53 % Favored : 89.86 % Rotamer: Outliers : 7.93 % Allowed : 24.94 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.02 (0.38), residues: 493 helix: 0.07 (0.40), residues: 158 sheet: -1.83 (0.52), residues: 85 loop : -2.13 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 456 TYR 0.014 0.002 TYR A 327 PHE 0.017 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 8701) covalent geometry : angle 0.63371 / 0.36 (12682) hydrogen bonds : bond 0.06237 / 4.09 ( 300) hydrogen bonds : angle 4.70879 / 3.23 ( 685) metal coordination : bond 0.00945 / 0.47 ( 4) metal coordination : angle 2.15056 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 155 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8571 (mmt180) REVERT: A 256 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: A 276 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7696 (mptt) outliers start: 34 outliers final: 21 residues processed: 89 average time/residue: 0.0947 time to fit residues: 10.8126 Evaluate side-chains 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** A 465 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 = 0.4076 r_free = 0.4076 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118932 restraints weight = 11010.032| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.43 r_work: 0.3362 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8705 Z= 0.131 Angle : 0.571 9.348 12685 Z= 0.328 Chirality : 0.037 0.253 1545 Planarity : 0.005 0.062 901 Dihedral : 23.957 179.963 3547 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.52 % Favored : 90.87 % Rotamer: Outliers : 5.83 % Allowed : 26.34 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.39), residues: 493 helix: 0.31 (0.41), residues: 160 sheet: -2.00 (0.52), residues: 90 loop : -1.84 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 37 TYR 0.013 0.001 TYR A 327 PHE 0.013 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 8701) covalent geometry : angle 0.57110 / 0.33 (12682) hydrogen bonds : bond 0.05638 / 3.75 ( 300) hydrogen bonds : angle 4.52984 / 3.09 ( 685) metal coordination : bond 0.00727 / 0.37 ( 4) metal coordination : angle 1.11933 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 141 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 386 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7221 (mtm180) outliers start: 25 outliers final: 16 residues processed: 82 average time/residue: 0.0883 time to fit residues: 9.6769 Evaluate side-chains 77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 333 HIS ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114921 restraints weight = 10959.211| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.49 r_work: 0.3306 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8705 Z= 0.214 Angle : 0.640 9.469 12685 Z= 0.361 Chirality : 0.042 0.389 1545 Planarity : 0.005 0.063 901 Dihedral : 23.955 177.781 3546 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.53 % Allowed : 27.04 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.88 (0.38), residues: 493 helix: 0.16 (0.40), residues: 158 sheet: -2.00 (0.52), residues: 90 loop : -1.89 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.017 0.002 TYR A 327 PHE 0.024 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 ( 8701) covalent geometry : angle 0.63891 / 0.36 (12682) hydrogen bonds : bond 0.06104 / 4.00 ( 300) hydrogen bonds : angle 4.52977 / 3.09 ( 685) metal coordination : bond 0.00615 / 0.31 ( 4) metal coordination : angle 2.35144 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 155 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (mmt180) REVERT: A 256 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: A 276 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7727 (mptt) REVERT: A 386 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7254 (mtm180) outliers start: 28 outliers final: 21 residues processed: 80 average time/residue: 0.0912 time to fit residues: 9.4522 Evaluate side-chains 82 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 62 optimal weight: 40.0000 chunk 33 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 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 = 0.4042 r_free = 0.4042 target = 0.164121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115705 restraints weight = 11017.781| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.50 r_work: 0.3317 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8705 Z= 0.186 Angle : 0.610 8.822 12685 Z= 0.347 Chirality : 0.041 0.392 1545 Planarity : 0.005 0.064 901 Dihedral : 23.969 178.057 3546 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.53 % Allowed : 27.51 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.38), residues: 493 helix: 0.24 (0.40), residues: 160 sheet: -1.93 (0.52), residues: 90 loop : -1.87 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.012 0.001 TYR A 340 PHE 0.019 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 8701) covalent geometry : angle 0.60983 / 0.35 (12682) hydrogen bonds : bond 0.05882 / 3.85 ( 300) hydrogen bonds : angle 4.51581 / 3.08 ( 685) metal coordination : bond 0.00541 / 0.27 ( 4) metal coordination : angle 1.93486 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 141 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 155 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8587 (mmt180) REVERT: A 256 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: A 386 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7259 (mtm180) outliers start: 28 outliers final: 22 residues processed: 79 average time/residue: 0.0837 time to fit residues: 8.7856 Evaluate side-chains 84 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN ** A 465 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 = 0.4055 r_free = 0.4055 target = 0.165278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116946 restraints weight = 10950.588| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.48 r_work: 0.3333 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8705 Z= 0.157 Angle : 0.595 9.360 12685 Z= 0.339 Chirality : 0.039 0.382 1545 Planarity : 0.005 0.062 901 Dihedral : 23.961 178.313 3546 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.74 % Favored : 89.66 % Rotamer: Outliers : 7.23 % Allowed : 27.04 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.39), residues: 493 helix: 0.30 (0.40), residues: 160 sheet: -1.88 (0.52), residues: 90 loop : -1.83 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.011 0.001 TYR A 340 PHE 0.018 0.001 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 8701) covalent geometry : angle 0.59473 / 0.34 (12682) hydrogen bonds : bond 0.05717 / 3.75 ( 300) hydrogen bonds : angle 4.45601 / 3.04 ( 685) metal coordination : bond 0.00578 / 0.29 ( 4) metal coordination : angle 1.61288 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: A 141 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (t) REVERT: A 155 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8561 (mmt180) REVERT: A 386 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7219 (mtm180) outliers start: 31 outliers final: 23 residues processed: 78 average time/residue: 0.0984 time to fit residues: 10.0624 Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 465 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 = 0.4025 r_free = 0.4025 target = 0.162646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114010 restraints weight = 10963.569| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.50 r_work: 0.3294 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8705 Z= 0.247 Angle : 0.654 8.952 12685 Z= 0.368 Chirality : 0.043 0.355 1545 Planarity : 0.005 0.063 901 Dihedral : 24.009 176.788 3546 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.53 % Favored : 89.86 % Rotamer: Outliers : 6.99 % Allowed : 27.04 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.38), residues: 493 helix: 0.14 (0.40), residues: 156 sheet: -1.86 (0.53), residues: 90 loop : -1.90 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.011 0.002 TYR A 340 PHE 0.025 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.25 ( 8701) covalent geometry : angle 0.65244 / 0.37 (12682) hydrogen bonds : bond 0.06251 / 4.08 ( 300) hydrogen bonds : angle 4.56162 / 3.11 ( 685) metal coordination : bond 0.00645 / 0.32 ( 4) metal coordination : angle 2.76314 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 141 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 155 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8614 (mmt180) REVERT: A 276 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7742 (mptt) REVERT: A 278 TRP cc_start: 0.8339 (m100) cc_final: 0.7989 (m100) REVERT: A 386 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7201 (mtm180) outliers start: 30 outliers final: 23 residues processed: 82 average time/residue: 0.1056 time to fit residues: 11.3503 Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN ** A 465 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 = 0.4065 r_free = 0.4065 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118007 restraints weight = 10895.652| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.48 r_work: 0.3349 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8705 Z= 0.143 Angle : 0.585 9.236 12685 Z= 0.332 Chirality : 0.038 0.365 1545 Planarity : 0.005 0.064 901 Dihedral : 23.949 178.495 3546 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.74 % Favored : 89.66 % Rotamer: Outliers : 5.13 % Allowed : 29.60 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.39), residues: 493 helix: 0.33 (0.40), residues: 160 sheet: -1.84 (0.52), residues: 90 loop : -1.81 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 456 TYR 0.011 0.001 TYR A 340 PHE 0.017 0.001 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 8701) covalent geometry : angle 0.58504 / 0.33 (12682) hydrogen bonds : bond 0.05559 / 3.67 ( 300) hydrogen bonds : angle 4.44324 / 3.03 ( 685) metal coordination : bond 0.00423 / 0.21 ( 4) metal coordination : angle 1.20856 / 0.62 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.156 Fit side-chains REVERT: A 53 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: A 73 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 141 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 155 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8565 (mmt180) REVERT: A 278 TRP cc_start: 0.8334 (m100) cc_final: 0.7989 (m100) REVERT: A 386 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7194 (mtm180) outliers start: 22 outliers final: 17 residues processed: 74 average time/residue: 0.1110 time to fit residues: 10.6404 Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 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 = 0.4070 r_free = 0.4070 target = 0.166628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118520 restraints weight = 10919.358| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.50 r_work: 0.3356 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8705 Z= 0.146 Angle : 0.575 9.537 12685 Z= 0.326 Chirality : 0.038 0.349 1545 Planarity : 0.005 0.063 901 Dihedral : 23.883 177.559 3546 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 5.59 % Allowed : 28.90 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.39), residues: 493 helix: 0.39 (0.40), residues: 161 sheet: -1.60 (0.56), residues: 80 loop : -1.78 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.012 0.001 TYR A 46 PHE 0.018 0.001 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 8701) covalent geometry : angle 0.57457 / 0.33 (12682) hydrogen bonds : bond 0.05441 / 3.63 ( 300) hydrogen bonds : angle 4.40515 / 3.00 ( 685) metal coordination : bond 0.00440 / 0.22 ( 4) metal coordination : angle 1.48001 / 0.75 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.85 seconds wall clock time: 41 minutes 3.65 seconds (2463.65 seconds total)