Starting phenix.real_space_refine on Wed Aug 5 02:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liq_63120/08_2026/9liq_63120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liq_63120/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9liq_63120/08_2026/9liq_63120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liq_63120/08_2026/9liq_63120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9liq_63120/08_2026/9liq_63120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liq_63120/08_2026/9liq_63120.map" } 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-2.2rc3-6140/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: 1.91, 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: 0.68 Conformation dependent library (CDL) restraints added in 253.8 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: 0.99 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: 1.51 Time building geometry restraints manager: 0.92 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: 11799 1.82 - 3.65: 804 3.65 - 5.47: 54 5.47 - 7.30: 17 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: 1085 0.047 - 0.095: 229 0.095 - 0.142: 205 0.142 - 0.189: 21 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: 3.630 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- 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= 0.303 Angle : 0.915 9.125 12685 Z= 0.712 Chirality : 0.061 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 0.00397 / 0.30 ( 8701) covalent geometry : angle 0.91405 / 0.71 (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 : 0.207 Fit side-chains REVERT: A 65 ASN cc_start: 0.7895 (m-40) cc_final: 0.7679 (m-40) REVERT: A 278 TRP cc_start: 0.8269 (m100) cc_final: 0.7753 (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: 0.1251 time to fit residues: 12.1251 Evaluate side-chains 74 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.158186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109933 restraints weight = 11007.326| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.49 r_work: 0.3227 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 8705 Z= 0.479 Angle : 1.023 9.517 12685 Z= 0.527 Chirality : 0.063 0.436 1545 Planarity : 0.009 0.097 901 Dihedral : 24.173 172.545 3553 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.95 % Favored : 88.24 % Rotamer: Outliers : 7.69 % Allowed : 26.81 % 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: -2.65 (0.37), residues: 493 helix: -0.65 (0.40), residues: 154 sheet: -1.84 (0.51), residues: 95 loop : -2.48 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 261 TYR 0.016 0.003 TYR A 327 PHE 0.029 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 0.00945 / 0.48 ( 8701) covalent geometry : angle 1.01917 / 0.53 (12682) hydrogen bonds : bond 0.09042 / 6.03 ( 300) hydrogen bonds : angle 5.45569 / 3.74 ( 685) metal coordination : bond 0.01233 / 0.61 ( 4) metal coordination : angle 5.97737 / 3.18 ( 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 96 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.195 Fit side-chains REVERT: A 37 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5432 (ptt-90) REVERT: A 143 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7889 (mttt) REVERT: A 250 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7650 (ptp-170) REVERT: A 256 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: A 276 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7695 (mptt) outliers start: 33 outliers final: 23 residues processed: 87 average time/residue: 0.1181 time to fit residues: 13.2406 Evaluate side-chains 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 423 LYS 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: 6.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.164944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116553 restraints weight = 10930.458| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.43 r_work: 0.3325 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1016 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= 0.148 Angle : 0.643 9.016 12685 Z= 0.362 Chirality : 0.041 0.252 1545 Planarity : 0.005 0.064 901 Dihedral : 24.034 174.972 3549 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.32 % Favored : 91.08 % Rotamer: Outliers : 5.36 % Allowed : 28.21 % 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: -2.17 (0.37), 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 327 PHE 0.014 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 0.00281 / 0.15 ( 8701) covalent geometry : angle 0.64286 / 0.36 (12682) hydrogen bonds : bond 0.06420 / 4.21 ( 300) hydrogen bonds : angle 4.85100 / 3.32 ( 685) metal coordination : bond 0.01361 / 0.68 ( 4) metal coordination : angle 1.31907 / 0.68 ( 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 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.210 Fit side-chains REVERT: A 73 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 276 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7673 (mptt) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.1106 time to fit residues: 11.6455 Evaluate side-chains 75 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 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 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 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: 0.0870 chunk 51 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4059 r_free = 0.4059 target = 0.165664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117456 restraints weight = 11112.274| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.43 r_work: 0.3339 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8705 Z= 0.146 Angle : 0.617 8.929 12685 Z= 0.343 Chirality : 0.040 0.247 1545 Planarity : 0.005 0.062 901 Dihedral : 23.878 175.509 3547 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.13 % Favored : 90.26 % 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: -1.89 (0.38), residues: 493 helix: 0.16 (0.40), residues: 160 sheet: -1.77 (0.52), residues: 85 loop : -2.04 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 456 TYR 0.015 0.001 TYR A 327 PHE 0.016 0.001 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 0.00283 / 0.15 ( 8701) covalent geometry : angle 0.61671 / 0.34 (12682) hydrogen bonds : bond 0.06065 / 4.04 ( 300) hydrogen bonds : angle 4.61502 / 3.15 ( 685) metal coordination : bond 0.00989 / 0.50 ( 4) metal coordination : angle 1.47241 / 0.75 ( 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 94 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.197 Fit side-chains REVERT: A 53 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.5948 (mp10) REVERT: A 73 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 155 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (mmt180) REVERT: A 276 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7700 (mptt) outliers start: 32 outliers final: 18 residues processed: 88 average time/residue: 0.1076 time to fit residues: 12.2069 Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.167130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119173 restraints weight = 10984.961| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.43 r_work: 0.3365 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8705 Z= 0.131 Angle : 0.600 9.580 12685 Z= 0.332 Chirality : 0.040 0.519 1545 Planarity : 0.005 0.061 901 Dihedral : 23.828 175.845 3547 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.52 % Favored : 90.87 % Rotamer: Outliers : 6.29 % Allowed : 26.34 % 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: -1.76 (0.39), residues: 493 helix: 0.30 (0.41), residues: 160 sheet: -1.97 (0.51), residues: 90 loop : -1.85 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.011 0.001 TYR A 340 PHE 0.012 0.002 PHE A 329 TRP 0.004 0.001 TRP A 161 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 8701) covalent geometry : angle 0.59963 / 0.33 (12682) hydrogen bonds : bond 0.05766 / 3.85 ( 300) hydrogen bonds : angle 4.47726 / 3.05 ( 685) metal coordination : bond 0.00862 / 0.43 ( 4) metal coordination : angle 1.28887 / 0.66 ( 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 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 155 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8469 (mmt180) REVERT: A 386 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7172 (mtm180) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 0.1151 time to fit residues: 12.1910 Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 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 143 LYS 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 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 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: 0.1980 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.162447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114026 restraints weight = 10975.489| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.49 r_work: 0.3292 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8705 Z= 0.245 Angle : 0.714 9.404 12685 Z= 0.383 Chirality : 0.046 0.318 1545 Planarity : 0.006 0.064 901 Dihedral : 23.878 174.379 3546 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.74 % Favored : 89.66 % Rotamer: Outliers : 7.46 % Allowed : 26.11 % 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: -1.91 (0.38), residues: 493 helix: 0.19 (0.40), residues: 155 sheet: -1.92 (0.53), residues: 90 loop : -1.97 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 151 TYR 0.012 0.002 TYR A 340 PHE 0.022 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 0.00493 / 0.24 ( 8701) covalent geometry : angle 0.71242 / 0.38 (12682) hydrogen bonds : bond 0.06554 / 4.30 ( 300) hydrogen bonds : angle 4.55456 / 3.10 ( 685) metal coordination : bond 0.00610 / 0.30 ( 4) metal coordination : angle 2.80020 / 1.49 ( 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 94 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 141 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (t) REVERT: A 155 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8606 (mmt180) REVERT: A 256 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: A 276 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7718 (mptt) REVERT: A 386 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7261 (mtm180) outliers start: 32 outliers final: 22 residues processed: 85 average time/residue: 0.1076 time to fit residues: 11.8962 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 : 0.214 ------------------------------------------------------------------------------- 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 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 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: 50.0000 chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.162567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114012 restraints weight = 11059.277| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.48 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8705 Z= 0.225 Angle : 0.695 8.353 12685 Z= 0.377 Chirality : 0.045 0.336 1545 Planarity : 0.005 0.063 901 Dihedral : 23.947 174.200 3546 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.53 % Favored : 89.86 % Rotamer: Outliers : 6.76 % Allowed : 27.27 % 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: 0.14 (0.40), residues: 156 sheet: -1.81 (0.51), residues: 100 loop : -2.00 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 456 TYR 0.011 0.002 TYR A 340 PHE 0.022 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/Z covalent geometry : bond 0.00447 / 0.22 ( 8701) covalent geometry : angle 0.69377 / 0.38 (12682) hydrogen bonds : bond 0.06430 / 4.21 ( 300) hydrogen bonds : angle 4.58338 / 3.12 ( 685) metal coordination : bond 0.00721 / 0.36 ( 4) metal coordination : angle 2.44294 / 1.30 ( 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 90 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 141 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 256 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: A 386 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7194 (mtm180) outliers start: 29 outliers final: 23 residues processed: 82 average time/residue: 0.1036 time to fit residues: 11.3978 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 : 0.202 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.166230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118066 restraints weight = 10936.667| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.49 r_work: 0.3351 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8705 Z= 0.140 Angle : 0.605 9.210 12685 Z= 0.336 Chirality : 0.039 0.312 1545 Planarity : 0.005 0.064 901 Dihedral : 23.879 175.260 3546 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.74 % Favored : 89.66 % 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: -1.69 (0.39), residues: 493 helix: 0.30 (0.40), residues: 160 sheet: -1.86 (0.52), residues: 90 loop : -1.79 (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 0.016 0.002 PHE A 329 TRP 0.005 0.001 TRP A 161 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 8701) covalent geometry : angle 0.60472 / 0.34 (12682) hydrogen bonds : bond 0.05736 / 3.81 ( 300) hydrogen bonds : angle 4.45624 / 3.04 ( 685) metal coordination : bond 0.00601 / 0.30 ( 4) metal coordination : angle 1.19139 / 0.61 ( 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 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: A 141 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 155 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8557 (mmt180) REVERT: A 256 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: A 386 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7128 (mtm180) outliers start: 29 outliers final: 20 residues processed: 83 average time/residue: 0.1121 time to fit residues: 12.2677 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 : 0.200 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.165163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116905 restraints weight = 10896.054| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.48 r_work: 0.3332 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1439 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= 0.167 Angle : 0.625 9.208 12685 Z= 0.343 Chirality : 0.041 0.271 1545 Planarity : 0.005 0.063 901 Dihedral : 23.848 175.101 3546 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.13 % Favored : 90.26 % Rotamer: Outliers : 6.06 % Allowed : 28.21 % 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: -1.68 (0.39), residues: 493 helix: 0.30 (0.40), residues: 158 sheet: -1.82 (0.52), residues: 90 loop : -1.78 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.011 0.001 TYR A 340 PHE 0.018 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 0.00326 / 0.17 ( 8701) covalent geometry : angle 0.62483 / 0.34 (12682) hydrogen bonds : bond 0.05827 / 3.86 ( 300) hydrogen bonds : angle 4.43020 / 3.02 ( 685) metal coordination : bond 0.00582 / 0.29 ( 4) metal coordination : angle 1.76425 / 0.91 ( 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 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 141 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (t) REVERT: A 155 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8572 (mmt180) REVERT: A 256 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: A 278 TRP cc_start: 0.8336 (m100) cc_final: 0.8003 (m100) REVERT: A 386 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7151 (mtm180) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.1103 time to fit residues: 11.4503 Evaluate side-chains 84 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.165276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117046 restraints weight = 10878.394| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.48 r_work: 0.3335 rms_B_bonded: 2.48 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: 0.8258 moved from start: 0.1449 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= 0.161 Angle : 0.622 9.276 12685 Z= 0.342 Chirality : 0.040 0.278 1545 Planarity : 0.005 0.063 901 Dihedral : 23.846 175.136 3546 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.29 % Allowed : 28.21 % 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: -1.66 (0.39), residues: 493 helix: 0.29 (0.40), residues: 158 sheet: -1.79 (0.52), residues: 90 loop : -1.77 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.011 0.001 TYR A 340 PHE 0.018 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 0.00316 / 0.16 ( 8701) covalent geometry : angle 0.62186 / 0.34 (12682) hydrogen bonds : bond 0.05785 / 3.83 ( 300) hydrogen bonds : angle 4.41896 / 3.01 ( 685) metal coordination : bond 0.00649 / 0.33 ( 4) metal coordination : angle 1.79680 / 0.93 ( 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 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 141 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8786 (t) REVERT: A 155 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8571 (mmt180) REVERT: A 256 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: A 278 TRP cc_start: 0.8350 (m100) cc_final: 0.8015 (m100) REVERT: A 386 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7153 (mtm180) outliers start: 27 outliers final: 22 residues processed: 80 average time/residue: 0.1127 time to fit residues: 11.8640 Evaluate side-chains 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.165665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117483 restraints weight = 10913.734| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.48 r_work: 0.3341 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1458 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= 0.147 Angle : 0.611 9.428 12685 Z= 0.337 Chirality : 0.039 0.265 1545 Planarity : 0.005 0.064 901 Dihedral : 23.845 175.227 3546 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.33 % Favored : 90.06 % Rotamer: Outliers : 6.06 % Allowed : 28.67 % 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: -1.64 (0.39), residues: 493 helix: 0.32 (0.40), residues: 160 sheet: -1.78 (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 0.011 0.001 TYR A 340 PHE 0.016 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 0.00285 / 0.15 ( 8701) covalent geometry : angle 0.61036 / 0.34 (12682) hydrogen bonds : bond 0.05719 / 3.79 ( 300) hydrogen bonds : angle 4.41479 / 3.00 ( 685) metal coordination : bond 0.00562 / 0.28 ( 4) metal coordination : angle 1.57108 / 0.81 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.35 seconds wall clock time: 44 minutes 14.46 seconds (2654.46 seconds total)