Starting phenix.real_space_refine on Thu Jul 2 00:16:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mms_48402/07_2026/9mms_48402.map" } resolution = 3.3 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= 0.003 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: 8 Type Number sf(0) Gaussians I 1 10.91 5 P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 2804 2.51 5 N 753 2.21 5 O 812 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2152 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2169 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 16, 'TRANS': 261} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.16, per 1000 atoms: 0.26 Number of scatterers: 4410 At special positions: 0 Unit cell: (63.51, 72.27, 87.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 1 52.95 S 31 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 812 8.00 N 753 7.00 C 2804 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: 0.43 Conformation dependent library (CDL) restraints added in 156.7 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1012 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 48.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.687A pdb=" N SER A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.920A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 573 " --> pdb=" O LEU A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.858A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 162 through 185 Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.042A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 241 through 258 removed outlier: 4.095A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.709A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 357 removed outlier: 4.242A pdb=" N LYS A 365 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A 354 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 363 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY A 356 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY A 361 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.689A pdb=" N GLN A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 76 removed outlier: 7.199A pdb=" N ILE B 71 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER B 86 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU B 73 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS B 84 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.680A pdb=" N GLY B 149 " --> pdb=" O VAL B 198 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 1755 1.39 - 1.55: 2678 1.55 - 1.71: 21 1.71 - 1.87: 50 1.87 - 2.03: 3 Bond restraints: 4507 Sorted by residual: bond pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3B AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " ideal model delta sigma weight residual 1.664 1.583 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C23 LCJ B 703 " pdb=" I01 LCJ B 703 " ideal model delta sigma weight residual 2.099 2.030 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 4502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5844 2.12 - 4.23: 195 4.23 - 6.35: 33 6.35 - 8.47: 14 8.47 - 10.59: 10 Bond angle restraints: 6096 Sorted by residual: angle pdb=" CA MET A 581 " pdb=" CB MET A 581 " pdb=" CG MET A 581 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CB ARG A 583 " pdb=" CG ARG A 583 " pdb=" CD ARG A 583 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CA GLU A 478 " pdb=" CB GLU A 478 " pdb=" CG GLU A 478 " ideal model delta sigma weight residual 114.10 121.47 -7.37 2.00e+00 2.50e-01 1.36e+01 angle pdb=" N GLN B 153 " pdb=" CA GLN B 153 " pdb=" C GLN B 153 " ideal model delta sigma weight residual 111.28 107.33 3.95 1.09e+00 8.42e-01 1.32e+01 angle pdb=" CA ILE B 196 " pdb=" CB ILE B 196 " pdb=" CG1 ILE B 196 " ideal model delta sigma weight residual 110.40 116.46 -6.06 1.70e+00 3.46e-01 1.27e+01 ... (remaining 6091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 2614 30.55 - 61.10: 120 61.10 - 91.65: 21 91.65 - 122.20: 4 122.20 - 152.75: 3 Dihedral angle restraints: 2762 sinusoidal: 1189 harmonic: 1573 Sorted by residual: dihedral pdb=" CD ARG B 227 " pdb=" NE ARG B 227 " pdb=" CZ ARG B 227 " pdb=" NH1 ARG B 227 " ideal model delta sinusoidal sigma weight residual 0.00 -40.69 40.69 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA TYR B 261 " pdb=" C TYR B 261 " pdb=" N PRO B 262 " pdb=" CA PRO B 262 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" O3A AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sinusoidal sigma weight residual -107.39 45.36 -152.75 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 2759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 503 0.053 - 0.106: 126 0.106 - 0.159: 31 0.159 - 0.212: 3 0.212 - 0.265: 2 Chirality restraints: 665 Sorted by residual: chirality pdb=" C3' AGS B 701 " pdb=" C2' AGS B 701 " pdb=" C4' AGS B 701 " pdb=" O3' AGS B 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' AGS A 701 " pdb=" C2' AGS A 701 " pdb=" C4' AGS A 701 " pdb=" O3' AGS A 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU B 155 " pdb=" CB LEU B 155 " pdb=" CD1 LEU B 155 " pdb=" CD2 LEU B 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 662 not shown) Planarity restraints: 766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 227 " 0.702 9.50e-02 1.11e+02 3.15e-01 6.05e+01 pdb=" NE ARG B 227 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 227 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 227 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 227 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 450 " 0.425 9.50e-02 1.11e+02 1.90e-01 2.22e+01 pdb=" NE ARG A 450 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 450 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 450 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 450 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 334 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C PHE B 334 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE B 334 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN B 335 " 0.016 2.00e-02 2.50e+03 ... (remaining 763 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.59: 61 2.59 - 3.18: 3979 3.18 - 3.77: 7633 3.77 - 4.37: 10798 4.37 - 4.96: 17419 Nonbonded interactions: 39890 Sorted by model distance: nonbonded pdb=" OD2 ASP B 208 " pdb="MG MG B 702 " model vdw 1.994 2.170 nonbonded pdb=" O1B AGS B 701 " pdb="MG MG B 702 " model vdw 2.029 2.170 nonbonded pdb=" O1B AGS A 701 " pdb="MG MG A 702 " model vdw 2.086 2.170 nonbonded pdb=" O SER B 228 " pdb=" OH TYR B 261 " model vdw 2.131 3.040 nonbonded pdb=" N GLU A 345 " pdb=" OE1 GLU A 345 " model vdw 2.171 3.120 ... (remaining 39885 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 4507 Z= 0.325 Angle : 0.981 10.587 6096 Z= 0.496 Chirality : 0.052 0.265 665 Planarity : 0.014 0.315 766 Dihedral : 18.670 152.750 1750 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.63 % Allowed : 23.48 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.34), residues: 540 helix: 0.36 (0.33), residues: 237 sheet: -1.46 (0.46), residues: 60 loop : -0.63 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 583 TYR 0.025 0.003 TYR A 574 PHE 0.041 0.002 PHE B 334 TRP 0.006 0.001 TRP A 511 HIS 0.003 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.32 ( 4507) covalent geometry : angle 0.98133 / 0.50 ( 6096) hydrogen bonds : bond 0.14566 / 9.25 ( 204) hydrogen bonds : angle 7.47467 / 5.13 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 TRP cc_start: 0.7520 (m100) cc_final: 0.7212 (m100) REVERT: B 219 MET cc_start: 0.6367 (tmt) cc_final: 0.5961 (tmm) REVERT: B 256 MET cc_start: 0.6726 (mmt) cc_final: 0.6437 (mmp) REVERT: B 354 GLN cc_start: 0.9188 (tt0) cc_final: 0.8756 (tm-30) outliers start: 3 outliers final: 1 residues processed: 107 average time/residue: 0.0828 time to fit residues: 10.7835 Evaluate side-chains 88 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 GLN ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.136351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.119704 restraints weight = 7319.868| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.16 r_work: 0.3847 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4507 Z= 0.152 Angle : 0.654 7.659 6096 Z= 0.327 Chirality : 0.044 0.202 665 Planarity : 0.005 0.041 766 Dihedral : 16.191 154.370 674 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.03 % Allowed : 18.03 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.34), residues: 540 helix: 0.71 (0.33), residues: 242 sheet: -0.98 (0.50), residues: 66 loop : -0.62 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 234 TYR 0.016 0.002 TYR A 532 PHE 0.020 0.002 PHE B 334 TRP 0.005 0.001 TRP A 511 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4507) covalent geometry : angle 0.65407 / 0.33 ( 6096) hydrogen bonds : bond 0.04549 / 2.96 ( 204) hydrogen bonds : angle 5.79698 / 4.01 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 447 ASP cc_start: 0.8147 (t0) cc_final: 0.7880 (t70) REVERT: A 496 TRP cc_start: 0.7796 (m100) cc_final: 0.7521 (m100) REVERT: B 219 MET cc_start: 0.6845 (tmt) cc_final: 0.6302 (tmm) REVERT: B 256 MET cc_start: 0.7129 (mmt) cc_final: 0.6797 (mmt) REVERT: B 354 GLN cc_start: 0.9030 (tt0) cc_final: 0.8764 (tm-30) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 0.0645 time to fit residues: 9.1519 Evaluate side-chains 99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.134508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.116852 restraints weight = 9379.682| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.65 r_work: 0.3799 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4507 Z= 0.144 Angle : 0.629 7.235 6096 Z= 0.320 Chirality : 0.043 0.138 665 Planarity : 0.005 0.044 766 Dihedral : 14.640 160.244 674 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.19 % Allowed : 19.08 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.35), residues: 540 helix: 0.75 (0.33), residues: 242 sheet: -0.51 (0.54), residues: 71 loop : -0.60 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 234 TYR 0.014 0.002 TYR A 458 PHE 0.014 0.002 PHE B 334 TRP 0.005 0.001 TRP A 511 HIS 0.005 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 4507) covalent geometry : angle 0.62926 / 0.32 ( 6096) hydrogen bonds : bond 0.04084 / 2.67 ( 204) hydrogen bonds : angle 5.57596 / 3.90 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 TYR cc_start: 0.8588 (t80) cc_final: 0.8246 (t80) REVERT: A 496 TRP cc_start: 0.7897 (m100) cc_final: 0.7693 (m100) REVERT: A 583 ARG cc_start: 0.8484 (tpm170) cc_final: 0.8278 (tpm170) REVERT: B 69 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 151 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6415 (tm) REVERT: B 219 MET cc_start: 0.6986 (tmt) cc_final: 0.6481 (tmm) REVERT: B 230 MET cc_start: 0.8072 (mmm) cc_final: 0.7298 (mmm) REVERT: B 256 MET cc_start: 0.7188 (mmt) cc_final: 0.6880 (mmt) REVERT: B 354 GLN cc_start: 0.9013 (tt0) cc_final: 0.8790 (tm-30) REVERT: B 356 MET cc_start: 0.8775 (mpt) cc_final: 0.8286 (mpp) outliers start: 20 outliers final: 13 residues processed: 109 average time/residue: 0.0537 time to fit residues: 7.6117 Evaluate side-chains 102 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.134542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118113 restraints weight = 7385.995| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.16 r_work: 0.3826 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4507 Z= 0.129 Angle : 0.597 8.392 6096 Z= 0.302 Chirality : 0.043 0.139 665 Planarity : 0.005 0.047 766 Dihedral : 14.598 172.617 674 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.35 % Allowed : 18.66 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.35), residues: 540 helix: 0.98 (0.34), residues: 236 sheet: -0.41 (0.55), residues: 71 loop : -0.56 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.021 0.002 TYR A 532 PHE 0.011 0.001 PHE A 487 TRP 0.005 0.001 TRP A 511 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4507) covalent geometry : angle 0.59712 / 0.30 ( 6096) hydrogen bonds : bond 0.03764 / 2.47 ( 204) hydrogen bonds : angle 5.36619 / 3.79 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7909 (tmm-80) cc_final: 0.7660 (tmm-80) REVERT: A 458 TYR cc_start: 0.8625 (t80) cc_final: 0.8385 (t80) REVERT: A 486 ASP cc_start: 0.7736 (m-30) cc_final: 0.7360 (m-30) REVERT: B 69 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 219 MET cc_start: 0.7078 (tmt) cc_final: 0.6296 (ttt) REVERT: B 256 MET cc_start: 0.7162 (mmt) cc_final: 0.6829 (mmt) REVERT: B 354 GLN cc_start: 0.9028 (tt0) cc_final: 0.8744 (tm-30) REVERT: B 356 MET cc_start: 0.8803 (mpt) cc_final: 0.8575 (mpt) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.0646 time to fit residues: 8.8448 Evaluate side-chains 105 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.114365 restraints weight = 9582.180| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.73 r_work: 0.3765 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4507 Z= 0.141 Angle : 0.619 13.705 6096 Z= 0.307 Chirality : 0.043 0.142 665 Planarity : 0.005 0.052 766 Dihedral : 14.096 173.168 673 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.98 % Allowed : 19.08 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.35), residues: 540 helix: 0.91 (0.33), residues: 237 sheet: -0.46 (0.55), residues: 71 loop : -0.57 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 583 TYR 0.021 0.002 TYR A 532 PHE 0.012 0.001 PHE A 487 TRP 0.006 0.001 TRP A 511 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4507) covalent geometry : angle 0.61887 / 0.31 ( 6096) hydrogen bonds : bond 0.03685 / 2.44 ( 204) hydrogen bonds : angle 5.30825 / 3.75 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5692 (ptp) cc_final: 0.5038 (ptp) REVERT: A 450 ARG cc_start: 0.7978 (tmm-80) cc_final: 0.7675 (tmm-80) REVERT: A 458 TYR cc_start: 0.8652 (t80) cc_final: 0.8413 (t80) REVERT: A 486 ASP cc_start: 0.7885 (m-30) cc_final: 0.7533 (m-30) REVERT: A 496 TRP cc_start: 0.7665 (m100) cc_final: 0.7371 (m100) REVERT: B 69 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 219 MET cc_start: 0.7250 (tmt) cc_final: 0.6452 (ttm) REVERT: B 256 MET cc_start: 0.7359 (mmt) cc_final: 0.6947 (mmt) REVERT: B 354 GLN cc_start: 0.9044 (tt0) cc_final: 0.8737 (tm-30) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.0612 time to fit residues: 8.3490 Evaluate side-chains 101 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN B 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.132735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.115894 restraints weight = 9337.408| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.62 r_work: 0.3778 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4507 Z= 0.128 Angle : 0.608 9.855 6096 Z= 0.305 Chirality : 0.042 0.132 665 Planarity : 0.005 0.053 766 Dihedral : 12.941 160.032 673 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.77 % Allowed : 20.34 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.35), residues: 540 helix: 0.94 (0.34), residues: 238 sheet: -0.44 (0.54), residues: 71 loop : -0.62 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 234 TYR 0.017 0.001 TYR A 532 PHE 0.010 0.001 PHE A 487 TRP 0.005 0.001 TRP A 511 HIS 0.008 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4507) covalent geometry : angle 0.60830 / 0.30 ( 6096) hydrogen bonds : bond 0.03601 / 2.41 ( 204) hydrogen bonds : angle 5.30260 / 3.75 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8684 (mmmm) REVERT: A 450 ARG cc_start: 0.7941 (tmm-80) cc_final: 0.7635 (tmm-80) REVERT: A 458 TYR cc_start: 0.8620 (t80) cc_final: 0.8402 (t80) REVERT: A 486 ASP cc_start: 0.7834 (m-30) cc_final: 0.7520 (m-30) REVERT: A 496 TRP cc_start: 0.7634 (m100) cc_final: 0.7409 (m100) REVERT: B 219 MET cc_start: 0.7211 (tmt) cc_final: 0.6443 (ttm) REVERT: B 256 MET cc_start: 0.7464 (mmt) cc_final: 0.7134 (mmt) REVERT: B 342 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6602 (mp) REVERT: B 354 GLN cc_start: 0.9002 (tt0) cc_final: 0.8800 (tm-30) REVERT: B 356 MET cc_start: 0.8644 (mmm) cc_final: 0.8309 (mpp) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.0609 time to fit residues: 8.2672 Evaluate side-chains 100 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.132248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.115640 restraints weight = 9229.507| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.59 r_work: 0.3780 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4507 Z= 0.134 Angle : 0.617 9.051 6096 Z= 0.309 Chirality : 0.042 0.194 665 Planarity : 0.005 0.055 766 Dihedral : 12.357 151.327 673 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.19 % Allowed : 20.13 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.35), residues: 540 helix: 0.99 (0.34), residues: 238 sheet: -0.25 (0.55), residues: 65 loop : -0.72 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 234 TYR 0.021 0.002 TYR A 532 PHE 0.010 0.001 PHE A 487 TRP 0.004 0.001 TRP A 511 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4507) covalent geometry : angle 0.61715 / 0.31 ( 6096) hydrogen bonds : bond 0.03640 / 2.40 ( 204) hydrogen bonds : angle 5.33631 / 3.78 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8688 (mmmm) REVERT: A 412 MET cc_start: 0.5854 (ptp) cc_final: 0.5158 (ptp) REVERT: A 450 ARG cc_start: 0.7931 (tmm-80) cc_final: 0.7605 (tmm-80) REVERT: A 486 ASP cc_start: 0.7822 (m-30) cc_final: 0.7526 (m-30) REVERT: A 496 TRP cc_start: 0.7846 (m100) cc_final: 0.7643 (m100) REVERT: B 219 MET cc_start: 0.7272 (tmt) cc_final: 0.6561 (ttt) REVERT: B 256 MET cc_start: 0.7493 (mmt) cc_final: 0.7168 (mmt) REVERT: B 308 MET cc_start: 0.6582 (ttp) cc_final: 0.6307 (ttp) REVERT: B 342 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6613 (mp) REVERT: B 356 MET cc_start: 0.8658 (mmm) cc_final: 0.8306 (mpp) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.0656 time to fit residues: 9.0634 Evaluate side-chains 101 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 0.0030 chunk 48 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117077 restraints weight = 9020.397| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.51 r_work: 0.3815 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4507 Z= 0.125 Angle : 0.643 8.743 6096 Z= 0.324 Chirality : 0.043 0.189 665 Planarity : 0.005 0.052 766 Dihedral : 11.969 145.345 673 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.56 % Allowed : 21.17 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.35), residues: 540 helix: 1.04 (0.34), residues: 238 sheet: -0.37 (0.54), residues: 71 loop : -0.60 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 234 TYR 0.031 0.002 TYR A 458 PHE 0.009 0.001 PHE B 360 TRP 0.003 0.001 TRP A 511 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 4507) covalent geometry : angle 0.64272 / 0.32 ( 6096) hydrogen bonds : bond 0.03643 / 2.39 ( 204) hydrogen bonds : angle 5.33420 / 3.77 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8721 (mmmm) REVERT: A 412 MET cc_start: 0.5778 (ptp) cc_final: 0.5107 (ptp) REVERT: A 450 ARG cc_start: 0.7912 (tmm-80) cc_final: 0.7615 (tmm-80) REVERT: A 496 TRP cc_start: 0.7800 (m100) cc_final: 0.7577 (m100) REVERT: B 145 HIS cc_start: 0.6749 (t-90) cc_final: 0.6540 (t-90) REVERT: B 219 MET cc_start: 0.7260 (tmt) cc_final: 0.6659 (ttt) REVERT: B 256 MET cc_start: 0.7503 (mmt) cc_final: 0.7189 (mmt) REVERT: B 308 MET cc_start: 0.6723 (ttp) cc_final: 0.6504 (ttp) REVERT: B 342 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6562 (mp) REVERT: B 356 MET cc_start: 0.8738 (mmm) cc_final: 0.8395 (mpp) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.0649 time to fit residues: 8.7002 Evaluate side-chains 103 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.132201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.115854 restraints weight = 8870.727| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.43 r_work: 0.3793 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4507 Z= 0.145 Angle : 0.657 8.309 6096 Z= 0.329 Chirality : 0.043 0.184 665 Planarity : 0.005 0.052 766 Dihedral : 11.933 143.333 673 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.14 % Allowed : 22.85 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.35), residues: 540 helix: 1.05 (0.34), residues: 238 sheet: -0.41 (0.57), residues: 66 loop : -0.66 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.024 0.002 TYR A 532 PHE 0.009 0.001 PHE B 360 TRP 0.014 0.001 TRP A 423 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4507) covalent geometry : angle 0.65724 / 0.33 ( 6096) hydrogen bonds : bond 0.03692 / 2.42 ( 204) hydrogen bonds : angle 5.46159 / 3.84 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8710 (mmmm) REVERT: A 450 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7634 (tmm-80) REVERT: B 219 MET cc_start: 0.7323 (tmt) cc_final: 0.6631 (ttm) REVERT: B 256 MET cc_start: 0.7577 (mmt) cc_final: 0.7260 (mmt) REVERT: B 342 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6681 (mp) REVERT: B 354 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 356 MET cc_start: 0.8724 (mmm) cc_final: 0.8379 (mpp) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.0527 time to fit residues: 6.9370 Evaluate side-chains 103 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 46 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** B 214 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 = 0.4202 r_free = 0.4202 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.116973 restraints weight = 9151.491| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.55 r_work: 0.3808 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4507 Z= 0.131 Angle : 0.658 8.553 6096 Z= 0.331 Chirality : 0.043 0.190 665 Planarity : 0.005 0.050 766 Dihedral : 11.711 139.621 673 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.52 % Allowed : 23.90 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.35), residues: 540 helix: 1.08 (0.34), residues: 238 sheet: -0.23 (0.56), residues: 65 loop : -0.67 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 113 TYR 0.047 0.002 TYR A 458 PHE 0.008 0.001 PHE A 487 TRP 0.007 0.001 TRP A 423 HIS 0.005 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4507) covalent geometry : angle 0.65826 / 0.33 ( 6096) hydrogen bonds : bond 0.03704 / 2.44 ( 204) hydrogen bonds : angle 5.46849 / 3.84 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7955 (tmm-80) cc_final: 0.7660 (tmm-80) REVERT: A 496 TRP cc_start: 0.7427 (m100) cc_final: 0.7108 (m100) REVERT: B 219 MET cc_start: 0.7286 (tmt) cc_final: 0.6705 (ttt) REVERT: B 256 MET cc_start: 0.7565 (mmt) cc_final: 0.7263 (mmt) REVERT: B 342 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6642 (mp) REVERT: B 354 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 356 MET cc_start: 0.8703 (mmm) cc_final: 0.8390 (mpp) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.0712 time to fit residues: 9.0550 Evaluate side-chains 100 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 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 = 0.4175 r_free = 0.4175 target = 0.131306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114944 restraints weight = 9244.974| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.56 r_work: 0.3779 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4507 Z= 0.149 Angle : 0.693 9.813 6096 Z= 0.345 Chirality : 0.044 0.188 665 Planarity : 0.005 0.050 766 Dihedral : 11.697 138.562 673 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.73 % Allowed : 23.90 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.35), residues: 540 helix: 1.01 (0.34), residues: 238 sheet: -0.41 (0.56), residues: 66 loop : -0.68 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.043 0.003 TYR A 458 PHE 0.011 0.001 PHE A 487 TRP 0.007 0.001 TRP A 423 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4507) covalent geometry : angle 0.69257 / 0.35 ( 6096) hydrogen bonds : bond 0.03764 / 2.48 ( 204) hydrogen bonds : angle 5.59494 / 3.95 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.48 seconds wall clock time: 19 minutes 54.66 seconds (1194.66 seconds total)