Starting phenix.real_space_refine on Tue Feb 3 15:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mms_48402/02_2026/9mms_48402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mms_48402/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mms_48402/02_2026/9mms_48402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mms_48402/02_2026/9mms_48402.map" model { file = "/net/cci-nas-00/data/ceres_data/9mms_48402/02_2026/9mms_48402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mms_48402/02_2026/9mms_48402.cif" } 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-2.0-5952/lib/python3.9/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: 0.82, per 1000 atoms: 0.19 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: 0.28 Conformation dependent library (CDL) restraints added in 197.5 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: 0.09 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: 0.41 Time building geometry restraints manager: 0.34 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=" 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 bond pdb=" C10 LCJ B 703 " pdb=" N07 LCJ B 703 " ideal model delta sigma weight residual 1.371 1.425 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" N TYR B 240 " pdb=" CA TYR B 240 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.50e+00 bond pdb=" N ARG B 201 " pdb=" CA ARG B 201 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.18e+00 bond pdb=" N HIS A 434 " pdb=" CA HIS A 434 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.14e+00 ... (remaining 4502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5883 2.12 - 4.23: 177 4.23 - 6.35: 26 6.35 - 8.47: 4 8.47 - 10.59: 6 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 - 29.04: 2591 29.04 - 58.07: 121 58.07 - 87.11: 10 87.11 - 116.15: 0 116.15 - 145.18: 4 Dihedral angle restraints: 2726 sinusoidal: 1153 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=" O1B 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 68.91 -76.27 145.18 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 2723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 440 0.040 - 0.079: 153 0.079 - 0.119: 52 0.119 - 0.159: 21 0.159 - 0.198: 3 Chirality restraints: 669 Sorted by residual: 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 chirality pdb=" CA MET A 350 " pdb=" N MET A 350 " pdb=" C MET A 350 " pdb=" CB MET A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA MET B 256 " pdb=" N MET B 256 " pdb=" C MET B 256 " pdb=" CB MET B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 666 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: 1.440 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.330 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.005 0.069 4507 Z= 0.269 Angle : 0.866 10.587 6096 Z= 0.473 Chirality : 0.050 0.198 669 Planarity : 0.014 0.315 766 Dihedral : 16.476 145.183 1714 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 covalent geometry : bond 0.00490 ( 4507) covalent geometry : angle 0.86650 ( 6096) hydrogen bonds : bond 0.14566 ( 204) hydrogen bonds : angle 7.47467 ( 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 : 0.113 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: 0.0697 time to fit residues: 9.1261 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 : 0.101 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.135316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.117613 restraints weight = 9513.283| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.72 r_work: 0.3798 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4507 Z= 0.167 Angle : 0.649 7.751 6096 Z= 0.333 Chirality : 0.045 0.194 669 Planarity : 0.005 0.041 766 Dihedral : 12.750 139.655 638 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.31 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: -0.15 (0.34), residues: 540 helix: 0.73 (0.33), residues: 240 sheet: -0.98 (0.50), residues: 66 loop : -0.60 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.016 0.002 TYR A 532 PHE 0.018 0.002 PHE B 334 TRP 0.005 0.001 TRP A 511 HIS 0.006 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4507) covalent geometry : angle 0.64918 ( 6096) hydrogen bonds : bond 0.04541 ( 204) hydrogen bonds : angle 5.85236 ( 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 122 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.8235 (t0) cc_final: 0.7980 (t70) REVERT: A 496 TRP cc_start: 0.7855 (m100) cc_final: 0.7601 (m100) REVERT: B 219 MET cc_start: 0.6959 (tmt) cc_final: 0.6364 (tmm) REVERT: B 256 MET cc_start: 0.7142 (mmt) cc_final: 0.6769 (mmt) REVERT: B 308 MET cc_start: 0.5808 (ttp) cc_final: 0.5473 (ttp) REVERT: B 354 GLN cc_start: 0.9035 (tt0) cc_final: 0.8723 (tm-30) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 0.0680 time to fit residues: 9.3573 Evaluate side-chains 98 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 357 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.135541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.117685 restraints weight = 9680.181| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.73 r_work: 0.3805 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4507 Z= 0.137 Angle : 0.626 8.003 6096 Z= 0.320 Chirality : 0.043 0.159 669 Planarity : 0.005 0.045 766 Dihedral : 12.501 139.837 638 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.77 % Allowed : 19.71 % Favored : 76.52 % 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: -0.05 (0.35), residues: 540 helix: 0.76 (0.33), residues: 242 sheet: -0.55 (0.54), residues: 71 loop : -0.62 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 234 TYR 0.023 0.002 TYR A 458 PHE 0.015 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 covalent geometry : bond 0.00309 ( 4507) covalent geometry : angle 0.62588 ( 6096) hydrogen bonds : bond 0.04166 ( 204) hydrogen bonds : angle 5.61654 ( 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 111 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7997 (ttmt) REVERT: A 458 TYR cc_start: 0.8372 (t80) cc_final: 0.8012 (t80) REVERT: A 496 TRP cc_start: 0.7885 (m100) cc_final: 0.7650 (m100) REVERT: B 151 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6372 (tm) REVERT: B 219 MET cc_start: 0.7012 (tmt) cc_final: 0.6483 (tmm) REVERT: B 230 MET cc_start: 0.8046 (mmm) cc_final: 0.7279 (mmm) REVERT: B 256 MET cc_start: 0.7218 (mmt) cc_final: 0.6846 (mmt) REVERT: B 354 GLN cc_start: 0.9056 (tt0) cc_final: 0.8784 (tm-30) REVERT: B 356 MET cc_start: 0.8749 (mpt) cc_final: 0.8277 (mpt) outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.0657 time to fit residues: 8.6536 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ARG 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 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 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: 2.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 48 optimal weight: 0.0070 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4233 r_free = 0.4233 target = 0.136430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.118892 restraints weight = 9349.298| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.70 r_work: 0.3823 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4507 Z= 0.119 Angle : 0.593 6.996 6096 Z= 0.303 Chirality : 0.042 0.141 669 Planarity : 0.005 0.047 766 Dihedral : 12.324 139.209 638 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.56 % Allowed : 18.45 % 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: 0.08 (0.35), residues: 540 helix: 0.93 (0.34), residues: 236 sheet: -0.40 (0.57), residues: 66 loop : -0.63 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 234 TYR 0.019 0.002 TYR A 532 PHE 0.009 0.001 PHE B 334 TRP 0.005 0.001 TRP A 511 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4507) covalent geometry : angle 0.59305 ( 6096) hydrogen bonds : bond 0.03859 ( 204) hydrogen bonds : angle 5.42954 ( 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 113 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 458 TYR cc_start: 0.8494 (t80) cc_final: 0.8202 (t80) REVERT: A 496 TRP cc_start: 0.7834 (m100) cc_final: 0.7623 (m100) REVERT: A 583 ARG cc_start: 0.8500 (tpm170) cc_final: 0.8293 (tpm170) REVERT: B 69 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 219 MET cc_start: 0.7031 (tmt) cc_final: 0.6228 (ttt) REVERT: B 230 MET cc_start: 0.7952 (mmm) cc_final: 0.7257 (mmm) REVERT: B 256 MET cc_start: 0.7014 (mmt) cc_final: 0.6621 (mmt) REVERT: B 354 GLN cc_start: 0.9021 (tt0) cc_final: 0.8819 (tm-30) REVERT: B 356 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8356 (mpp) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.0740 time to fit residues: 9.7871 Evaluate side-chains 107 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ARG 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 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 Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.135216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117616 restraints weight = 9501.018| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.74 r_work: 0.3803 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4507 Z= 0.132 Angle : 0.587 5.909 6096 Z= 0.301 Chirality : 0.042 0.148 669 Planarity : 0.005 0.052 766 Dihedral : 12.203 138.802 638 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.14 (0.35), residues: 540 helix: 1.01 (0.34), residues: 236 sheet: -0.49 (0.54), residues: 71 loop : -0.58 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.010 0.002 TYR A 364 PHE 0.010 0.001 PHE A 487 TRP 0.007 0.001 TRP A 511 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4507) covalent geometry : angle 0.58694 ( 6096) hydrogen bonds : bond 0.03752 ( 204) hydrogen bonds : angle 5.30759 ( 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 115 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 TYR cc_start: 0.8592 (t80) cc_final: 0.8128 (t80) REVERT: A 570 LEU cc_start: 0.8434 (mm) cc_final: 0.8152 (mp) REVERT: A 583 ARG cc_start: 0.8542 (tpm170) cc_final: 0.8313 (tpm170) REVERT: B 151 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6493 (tm) REVERT: B 155 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6534 (mm) REVERT: B 219 MET cc_start: 0.7073 (tmt) cc_final: 0.6276 (ttt) REVERT: B 234 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6941 (mtp85) REVERT: B 256 MET cc_start: 0.7128 (mmt) cc_final: 0.6693 (mmt) REVERT: B 354 GLN cc_start: 0.9008 (tt0) cc_final: 0.8803 (tm-30) REVERT: B 356 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8362 (mpp) outliers start: 20 outliers final: 13 residues processed: 105 average time/residue: 0.0583 time to fit residues: 7.9061 Evaluate side-chains 102 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 94 MET 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 155 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 Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.134343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.116651 restraints weight = 9776.405| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.78 r_work: 0.3784 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4507 Z= 0.135 Angle : 0.625 14.229 6096 Z= 0.312 Chirality : 0.042 0.145 669 Planarity : 0.004 0.053 766 Dihedral : 12.142 138.237 637 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.40 % Allowed : 19.71 % 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: 0.10 (0.35), residues: 540 helix: 0.97 (0.34), residues: 236 sheet: -0.47 (0.54), residues: 71 loop : -0.61 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.018 0.002 TYR A 532 PHE 0.009 0.001 PHE A 487 TRP 0.010 0.001 TRP A 496 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4507) covalent geometry : angle 0.62497 ( 6096) hydrogen bonds : bond 0.03725 ( 204) hydrogen bonds : angle 5.34704 ( 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 114 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 TYR cc_start: 0.8604 (t80) cc_final: 0.8164 (t80) REVERT: A 486 ASP cc_start: 0.7838 (m-30) cc_final: 0.7473 (m-30) REVERT: A 570 LEU cc_start: 0.8429 (mm) cc_final: 0.8113 (mp) REVERT: A 583 ARG cc_start: 0.8533 (tpm170) cc_final: 0.8299 (tpm170) REVERT: B 69 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: B 155 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6538 (mm) REVERT: B 219 MET cc_start: 0.7182 (tmt) cc_final: 0.6408 (ttt) REVERT: B 230 MET cc_start: 0.8148 (mmm) cc_final: 0.7291 (mmm) REVERT: B 256 MET cc_start: 0.7233 (mmt) cc_final: 0.6802 (mmt) REVERT: B 354 GLN cc_start: 0.8995 (tt0) cc_final: 0.8788 (tm-30) REVERT: B 356 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8389 (mpp) outliers start: 21 outliers final: 15 residues processed: 106 average time/residue: 0.0522 time to fit residues: 7.1908 Evaluate side-chains 105 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 119 HIS Chi-restraints excluded: chain B residue 155 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 Chi-restraints excluded: chain B residue 356 MET 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: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4162 r_free = 0.4162 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.113816 restraints weight = 9497.463| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.66 r_work: 0.3745 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4507 Z= 0.167 Angle : 0.639 9.211 6096 Z= 0.324 Chirality : 0.044 0.144 669 Planarity : 0.005 0.055 766 Dihedral : 12.069 136.870 637 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.03 % Allowed : 20.13 % Favored : 74.84 % 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 (0.34), residues: 540 helix: 1.00 (0.33), residues: 236 sheet: -0.31 (0.56), residues: 65 loop : -0.70 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.026 0.002 TYR A 532 PHE 0.014 0.002 PHE A 487 TRP 0.010 0.001 TRP A 496 HIS 0.007 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4507) covalent geometry : angle 0.63945 ( 6096) hydrogen bonds : bond 0.03778 ( 204) hydrogen bonds : angle 5.34110 ( 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 122 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 TYR cc_start: 0.8709 (t80) cc_final: 0.8321 (t80) REVERT: A 486 ASP cc_start: 0.7968 (m-30) cc_final: 0.7662 (m-30) REVERT: A 583 ARG cc_start: 0.8679 (tpm170) cc_final: 0.8438 (tpm170) REVERT: B 69 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: B 74 LEU cc_start: 0.7573 (mt) cc_final: 0.7312 (mt) REVERT: B 219 MET cc_start: 0.7290 (tmt) cc_final: 0.6539 (ttt) REVERT: B 256 MET cc_start: 0.7445 (mmt) cc_final: 0.7121 (mmt) REVERT: B 342 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6587 (mp) REVERT: B 354 GLN cc_start: 0.9005 (tt0) cc_final: 0.8708 (tm-30) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.0619 time to fit residues: 8.8333 Evaluate side-chains 105 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.0010 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4186 r_free = 0.4186 target = 0.132762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.115973 restraints weight = 9376.319| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.67 r_work: 0.3778 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4507 Z= 0.136 Angle : 0.666 9.682 6096 Z= 0.331 Chirality : 0.043 0.174 669 Planarity : 0.005 0.054 766 Dihedral : 12.057 137.536 637 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.98 % Allowed : 22.01 % 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: 0.00 (0.34), residues: 540 helix: 0.90 (0.33), residues: 237 sheet: -0.34 (0.56), residues: 65 loop : -0.75 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 234 TYR 0.054 0.002 TYR A 532 PHE 0.012 0.001 PHE A 487 TRP 0.012 0.001 TRP A 496 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4507) covalent geometry : angle 0.66635 ( 6096) hydrogen bonds : bond 0.03633 ( 204) hydrogen bonds : angle 5.37774 ( 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 112 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8751 (mmmm) REVERT: A 458 TYR cc_start: 0.8633 (t80) cc_final: 0.8257 (t80) REVERT: A 583 ARG cc_start: 0.8624 (tpm170) cc_final: 0.8360 (tpm170) REVERT: A 590 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8093 (ttmt) REVERT: B 69 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 219 MET cc_start: 0.7219 (tmt) cc_final: 0.6534 (ttt) REVERT: B 256 MET cc_start: 0.7494 (mmt) cc_final: 0.7166 (mmt) REVERT: B 342 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6583 (mp) REVERT: B 354 GLN cc_start: 0.9028 (tt0) cc_final: 0.8705 (tm-30) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.0587 time to fit residues: 7.7031 Evaluate side-chains 105 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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 209 PHE 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 356 MET 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: 0.2980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.112907 restraints weight = 9493.604| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.63 r_work: 0.3732 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4507 Z= 0.184 Angle : 0.704 8.809 6096 Z= 0.346 Chirality : 0.045 0.201 669 Planarity : 0.005 0.054 766 Dihedral : 12.012 136.666 637 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.77 % Allowed : 21.80 % Favored : 74.42 % 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 (0.34), residues: 540 helix: 0.78 (0.33), residues: 237 sheet: -0.32 (0.57), residues: 65 loop : -0.81 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.035 0.003 TYR A 532 PHE 0.012 0.002 PHE B 360 TRP 0.010 0.002 TRP A 496 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 4507) covalent geometry : angle 0.70411 ( 6096) hydrogen bonds : bond 0.03806 ( 204) hydrogen bonds : angle 5.49350 ( 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 110 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8794 (mmmm) REVERT: A 486 ASP cc_start: 0.7982 (m-30) cc_final: 0.7716 (m-30) REVERT: A 583 ARG cc_start: 0.8663 (tpm170) cc_final: 0.8401 (tpm170) REVERT: B 219 MET cc_start: 0.7440 (tmt) cc_final: 0.6741 (ttt) REVERT: B 256 MET cc_start: 0.7611 (mmt) cc_final: 0.7162 (mmt) REVERT: B 342 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6611 (mp) REVERT: B 354 GLN cc_start: 0.9020 (tt0) cc_final: 0.8704 (tm-30) outliers start: 18 outliers final: 13 residues processed: 102 average time/residue: 0.0770 time to fit residues: 9.9626 Evaluate side-chains 102 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 MET 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: 0.7980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.131146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.114527 restraints weight = 9444.508| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.55 r_work: 0.3764 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 4507 Z= 0.148 Angle : 0.694 8.678 6096 Z= 0.341 Chirality : 0.045 0.214 669 Planarity : 0.005 0.052 766 Dihedral : 12.003 137.129 637 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.14 % Allowed : 22.64 % Favored : 74.21 % 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 (0.34), residues: 540 helix: 0.82 (0.33), residues: 237 sheet: -0.18 (0.58), residues: 63 loop : -0.87 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 450 TYR 0.046 0.002 TYR A 532 PHE 0.009 0.001 PHE B 360 TRP 0.006 0.001 TRP A 496 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4507) covalent geometry : angle 0.69399 ( 6096) hydrogen bonds : bond 0.03619 ( 204) hydrogen bonds : angle 5.49278 ( 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 107 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8748 (mmmm) REVERT: A 458 TYR cc_start: 0.8600 (t80) cc_final: 0.8299 (t80) REVERT: A 486 ASP cc_start: 0.7882 (m-30) cc_final: 0.7622 (m-30) REVERT: A 542 MET cc_start: 0.7718 (mmm) cc_final: 0.7498 (mmm) REVERT: B 219 MET cc_start: 0.7405 (tmt) cc_final: 0.6738 (ttt) REVERT: B 256 MET cc_start: 0.7579 (mmt) cc_final: 0.7185 (mmt) REVERT: B 342 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6661 (mp) REVERT: B 354 GLN cc_start: 0.8961 (tt0) cc_final: 0.8655 (tm-30) outliers start: 15 outliers final: 14 residues processed: 98 average time/residue: 0.0749 time to fit residues: 9.3617 Evaluate side-chains 103 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 A residue 570 LEU 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 195 ASN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 MET 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: 0.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.130051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.113248 restraints weight = 9506.041| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.66 r_work: 0.3746 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4507 Z= 0.153 Angle : 0.709 8.531 6096 Z= 0.352 Chirality : 0.045 0.209 669 Planarity : 0.005 0.051 766 Dihedral : 11.962 137.083 637 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.77 % Allowed : 22.01 % Favored : 74.21 % 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: -0.16 (0.34), residues: 540 helix: 0.76 (0.33), residues: 237 sheet: -0.27 (0.57), residues: 63 loop : -0.88 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.040 0.002 TYR A 532 PHE 0.009 0.001 PHE B 360 TRP 0.007 0.001 TRP A 496 HIS 0.002 0.001 HIS A 369 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4507) covalent geometry : angle 0.70931 ( 6096) hydrogen bonds : bond 0.03670 ( 204) hydrogen bonds : angle 5.48440 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1081.08 seconds wall clock time: 19 minutes 21.92 seconds (1161.92 seconds total)