Starting phenix.real_space_refine on Wed Feb 4 00:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liq_63120/02_2026/9liq_63120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liq_63120/02_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_63120/02_2026/9liq_63120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liq_63120/02_2026/9liq_63120.map" model { file = "/net/cci-nas-00/data/ceres_data/9liq_63120/02_2026/9liq_63120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liq_63120/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.93, per 1000 atoms: 0.24 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: 0.54 Conformation dependent library (CDL) restraints added in 146.6 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: 0.90 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: 1.23 Time building geometry restraints manager: 0.77 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=" 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=" CG1 ILE A 25 " pdb=" CD1 ILE A 25 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CB ILE A 302 " pdb=" CG2 ILE A 302 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" C ALA A 414 " pdb=" N ALA A 415 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.41e-02 5.03e+03 1.31e+00 bond pdb=" CG1 ILE A 346 " pdb=" CD1 ILE A 346 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.20e+00 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12278 1.82 - 3.65: 327 3.65 - 5.47: 54 5.47 - 7.30: 15 7.30 - 9.12: 8 Bond angle restraints: 12682 Sorted by residual: angle pdb=" CA LYS A 291 " pdb=" CB LYS A 291 " pdb=" CG LYS A 291 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C3' U B 29 " pdb=" O3' U B 29 " pdb=" P G B 30 " ideal model delta sigma weight residual 120.20 125.51 -5.31 1.50e+00 4.44e-01 1.25e+01 angle pdb=" C ARG A 151 " pdb=" N PHE A 152 " pdb=" CA PHE A 152 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C3' U B 192 " pdb=" O3' U B 192 " pdb=" P A B 193 " ideal model delta sigma weight residual 120.20 125.24 -5.04 1.50e+00 4.44e-01 1.13e+01 angle pdb=" C THR A 17 " pdb=" N THR A 18 " pdb=" CA THR A 18 " ideal model delta sigma weight residual 121.71 117.17 4.54 1.39e+00 5.18e-01 1.07e+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: 1293 0.047 - 0.095: 194 0.095 - 0.142: 42 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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= 0.188 Angle : 0.764 9.125 12685 Z= 0.396 Chirality : 0.040 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 covalent geometry : bond 0.00375 ( 8701) covalent geometry : angle 0.76329 (12682) hydrogen bonds : bond 0.14113 ( 300) hydrogen bonds : angle 6.56733 ( 685) metal coordination : bond 0.01670 ( 4) metal coordination : angle 2.09811 ( 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 : 0.197 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: 0.1160 time to fit residues: 11.1811 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 : 0.172 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 333 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109749 restraints weight = 11184.513| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.57 r_work: 0.3222 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 8705 Z= 0.440 Angle : 0.913 7.995 12685 Z= 0.464 Chirality : 0.050 0.301 1545 Planarity : 0.008 0.073 901 Dihedral : 24.163 175.185 3556 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 1.01 % Allowed : 10.34 % Favored : 88.64 % Rotamer: Outliers : 7.46 % Allowed : 27.04 % 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: -2.42 (0.37), residues: 493 helix: -0.47 (0.40), residues: 155 sheet: -1.81 (0.51), residues: 95 loop : -2.29 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 151 TYR 0.015 0.002 TYR A 327 PHE 0.025 0.003 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.011 0.002 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00893 ( 8701) covalent geometry : angle 0.90952 (12682) hydrogen bonds : bond 0.07602 ( 300) hydrogen bonds : angle 5.18656 ( 685) metal coordination : bond 0.01142 ( 4) metal coordination : angle 5.11036 ( 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 100 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.198 Fit side-chains REVERT: A 37 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5727 (ptt-90) REVERT: A 65 ASN cc_start: 0.8081 (m-40) cc_final: 0.7856 (m-40) REVERT: A 143 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: A 250 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (ptp-170) REVERT: A 256 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 276 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7665 (mptt) outliers start: 32 outliers final: 21 residues processed: 91 average time/residue: 0.1241 time to fit residues: 14.3680 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 : 0.199 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117601 restraints weight = 10952.849| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.44 r_work: 0.3340 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8705 Z= 0.157 Angle : 0.676 8.887 12685 Z= 0.345 Chirality : 0.038 0.188 1545 Planarity : 0.005 0.063 901 Dihedral : 23.909 179.084 3548 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.72 % Favored : 90.67 % Rotamer: Outliers : 6.06 % Allowed : 27.97 % 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: -1.93 (0.38), residues: 493 helix: 0.04 (0.40), residues: 160 sheet: -1.80 (0.52), residues: 85 loop : -1.99 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 261 TYR 0.013 0.002 TYR A 340 PHE 0.018 0.002 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8701) covalent geometry : angle 0.67529 (12682) hydrogen bonds : bond 0.05394 ( 300) hydrogen bonds : angle 4.64425 ( 685) metal coordination : bond 0.00937 ( 4) metal coordination : angle 1.87320 ( 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 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 155 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8560 (mmt180) REVERT: A 276 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7708 (mptt) outliers start: 26 outliers final: 16 residues processed: 81 average time/residue: 0.1147 time to fit residues: 11.9659 Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 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 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 262 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.0970 chunk 51 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4051 r_free = 0.4051 target = 0.164950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116590 restraints weight = 11120.434| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.49 r_work: 0.3325 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8705 Z= 0.181 Angle : 0.673 9.179 12685 Z= 0.343 Chirality : 0.038 0.208 1545 Planarity : 0.005 0.064 901 Dihedral : 23.868 178.789 3547 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.29 % Allowed : 26.81 % Favored : 66.90 % 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: -1.83 (0.38), residues: 493 helix: 0.16 (0.40), residues: 160 sheet: -1.59 (0.51), residues: 95 loop : -2.02 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.028 0.002 TYR A 327 PHE 0.018 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8701) covalent geometry : angle 0.67221 (12682) hydrogen bonds : bond 0.05326 ( 300) hydrogen bonds : angle 4.51666 ( 685) metal coordination : bond 0.00867 ( 4) metal coordination : angle 1.64621 ( 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 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5687 (ptt-90) REVERT: A 73 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 155 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8559 (mmt180) REVERT: A 256 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6639 (mm-30) outliers start: 27 outliers final: 18 residues processed: 84 average time/residue: 0.1180 time to fit residues: 12.6504 Evaluate side-chains 80 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 37 ARG 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 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 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 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: 0.9980 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4073 r_free = 0.4073 target = 0.166837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118554 restraints weight = 11000.745| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.50 r_work: 0.3353 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1201 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= 0.140 Angle : 0.654 9.624 12685 Z= 0.332 Chirality : 0.038 0.389 1545 Planarity : 0.005 0.063 901 Dihedral : 23.856 179.220 3546 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.92 % Favored : 90.47 % Rotamer: Outliers : 7.93 % Allowed : 25.64 % 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: -1.67 (0.39), residues: 493 helix: 0.32 (0.40), residues: 160 sheet: -1.88 (0.52), residues: 90 loop : -1.77 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.028 0.002 TYR A 327 PHE 0.011 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 covalent geometry : bond 0.00275 ( 8701) covalent geometry : angle 0.65362 (12682) hydrogen bonds : bond 0.05203 ( 300) hydrogen bonds : angle 4.38373 ( 685) metal coordination : bond 0.00674 ( 4) metal coordination : angle 1.22217 ( 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 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 141 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 155 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (mmt180) REVERT: A 256 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6693 (mm-30) outliers start: 34 outliers final: 22 residues processed: 83 average time/residue: 0.1076 time to fit residues: 11.6078 Evaluate side-chains 80 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 143 LYS 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 273 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.160347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111668 restraints weight = 11038.376| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.51 r_work: 0.3256 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8705 Z= 0.347 Angle : 0.808 8.486 12685 Z= 0.411 Chirality : 0.045 0.368 1545 Planarity : 0.006 0.064 901 Dihedral : 24.044 176.030 3546 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.84 % Rotamer: Outliers : 7.23 % Allowed : 25.41 % Favored : 67.37 % 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: -0.10 (0.40), residues: 155 sheet: -1.72 (0.53), residues: 95 loop : -2.01 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 151 TYR 0.014 0.002 TYR A 327 PHE 0.023 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.002 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 8701) covalent geometry : angle 0.80618 (12682) hydrogen bonds : bond 0.06544 ( 300) hydrogen bonds : angle 4.66594 ( 685) metal coordination : bond 0.00762 ( 4) metal coordination : angle 3.61676 ( 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 93 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: A 141 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8826 (t) REVERT: A 256 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6733 (mm-30) outliers start: 31 outliers final: 23 residues processed: 85 average time/residue: 0.0925 time to fit residues: 10.4244 Evaluate side-chains 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 52 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 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 331 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 62 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4038 r_free = 0.4038 target = 0.163752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115538 restraints weight = 11005.215| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.48 r_work: 0.3312 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8705 Z= 0.195 Angle : 0.698 8.404 12685 Z= 0.356 Chirality : 0.039 0.343 1545 Planarity : 0.005 0.064 901 Dihedral : 23.964 178.921 3546 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % 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: -1.85 (0.38), residues: 493 helix: 0.14 (0.40), residues: 157 sheet: -1.86 (0.53), residues: 90 loop : -1.89 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 456 TYR 0.013 0.002 TYR A 327 PHE 0.015 0.002 PHE A 329 TRP 0.006 0.001 TRP A 161 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8701) covalent geometry : angle 0.69795 (12682) hydrogen bonds : bond 0.05446 ( 300) hydrogen bonds : angle 4.50838 ( 685) metal coordination : bond 0.00708 ( 4) metal coordination : angle 1.56300 ( 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 92 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 138 LYS cc_start: 0.7553 (ttmm) cc_final: 0.7266 (mtpp) REVERT: A 141 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8789 (t) REVERT: A 155 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8619 (mmt180) REVERT: A 256 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: A 386 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7194 (mtm180) outliers start: 30 outliers final: 20 residues processed: 86 average time/residue: 0.1009 time to fit residues: 11.3502 Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 331 GLU 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 476 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4066 r_free = 0.4066 target = 0.166203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118000 restraints weight = 10930.675| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.49 r_work: 0.3349 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8705 Z= 0.155 Angle : 0.656 9.497 12685 Z= 0.332 Chirality : 0.037 0.298 1545 Planarity : 0.005 0.063 901 Dihedral : 23.862 178.687 3546 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.76 % Allowed : 26.81 % 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: -1.65 (0.39), residues: 493 helix: 0.36 (0.41), residues: 159 sheet: -1.78 (0.52), residues: 90 loop : -1.80 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.033 0.002 TYR A 327 PHE 0.014 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 covalent geometry : bond 0.00311 ( 8701) covalent geometry : angle 0.65534 (12682) hydrogen bonds : bond 0.05086 ( 300) hydrogen bonds : angle 4.40183 ( 685) metal coordination : bond 0.00580 ( 4) metal coordination : angle 1.15973 ( 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 90 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 138 LYS cc_start: 0.7522 (ttmm) cc_final: 0.7229 (mtpp) REVERT: A 141 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8766 (t) REVERT: A 155 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8567 (mmt180) REVERT: A 256 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: A 386 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7152 (mtm180) outliers start: 29 outliers final: 21 residues processed: 85 average time/residue: 0.1189 time to fit residues: 12.9681 Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 52 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 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 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: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4022 r_free = 0.4022 target = 0.162353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113790 restraints weight = 10938.249| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.48 r_work: 0.3287 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8705 Z= 0.264 Angle : 0.731 8.753 12685 Z= 0.373 Chirality : 0.041 0.268 1545 Planarity : 0.005 0.064 901 Dihedral : 23.932 175.939 3546 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % 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: -1.80 (0.39), residues: 493 helix: 0.17 (0.40), residues: 155 sheet: -1.58 (0.54), residues: 95 loop : -1.94 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 151 TYR 0.025 0.002 TYR A 327 PHE 0.021 0.002 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8701) covalent geometry : angle 0.72996 (12682) hydrogen bonds : bond 0.05749 ( 300) hydrogen bonds : angle 4.51732 ( 685) metal coordination : bond 0.00570 ( 4) metal coordination : angle 2.73792 ( 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 : 0.243 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 138 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7301 (mtpp) REVERT: A 141 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8805 (t) REVERT: A 155 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8659 (mmt180) REVERT: A 256 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: A 386 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7152 (mtm180) outliers start: 30 outliers final: 24 residues processed: 83 average time/residue: 0.0987 time to fit residues: 10.6891 Evaluate side-chains 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 52 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 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 GLU 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 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: 3.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4068 r_free = 0.4068 target = 0.166396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118162 restraints weight = 10831.915| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.49 r_work: 0.3349 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1546 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= 0.149 Angle : 0.652 9.403 12685 Z= 0.331 Chirality : 0.037 0.282 1545 Planarity : 0.005 0.062 901 Dihedral : 23.834 177.287 3546 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.53 % Favored : 89.86 % Rotamer: Outliers : 6.76 % Allowed : 27.74 % 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: -1.63 (0.39), residues: 493 helix: 0.36 (0.41), residues: 157 sheet: -1.79 (0.52), residues: 91 loop : -1.75 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.019 0.001 TYR A 327 PHE 0.012 0.001 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8701) covalent geometry : angle 0.65195 (12682) hydrogen bonds : bond 0.04992 ( 300) hydrogen bonds : angle 4.38894 ( 685) metal coordination : bond 0.00640 ( 4) metal coordination : angle 1.38481 ( 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 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 138 LYS cc_start: 0.7544 (ttmm) cc_final: 0.7246 (mtpp) REVERT: A 141 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8737 (t) REVERT: A 155 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8566 (mmt180) REVERT: A 256 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: A 386 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7117 (mtm180) outliers start: 29 outliers final: 24 residues processed: 81 average time/residue: 0.1095 time to fit residues: 11.6210 Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 52 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 298 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 GLU 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 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 21 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4064 r_free = 0.4064 target = 0.166057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117652 restraints weight = 10875.183| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.50 r_work: 0.3343 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1577 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= 0.161 Angle : 0.651 9.560 12685 Z= 0.331 Chirality : 0.037 0.266 1545 Planarity : 0.005 0.063 901 Dihedral : 23.787 175.496 3546 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.99 % Allowed : 27.27 % 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: -1.52 (0.39), residues: 493 helix: 0.34 (0.41), residues: 159 sheet: -1.44 (0.59), residues: 76 loop : -1.77 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.021 0.001 TYR A 327 PHE 0.013 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 covalent geometry : bond 0.00323 ( 8701) covalent geometry : angle 0.65051 (12682) hydrogen bonds : bond 0.05016 ( 300) hydrogen bonds : angle 4.36246 ( 685) metal coordination : bond 0.00718 ( 4) metal coordination : angle 1.52471 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.48 seconds wall clock time: 44 minutes 12.55 seconds (2652.55 seconds total)