Starting phenix.real_space_refine on Wed Feb 12 00:44:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.map" model { file = "/net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8in8_35592/02_2025/8in8_35592.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.072 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4098 2.51 5 N 1140 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2009 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3685 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 441} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "J" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 462 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.41, per 1000 atoms: 0.66 Number of scatterers: 6663 At special positions: 0 Unit cell: (71.6214, 87.0336, 107.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 47 15.00 Mg 1 11.99 O 1355 8.00 N 1140 7.00 C 4098 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: 1.96 Conformation dependent library (CDL) restraints added in 658.4 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.0% alpha, 20.7% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'B' and resid 356 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.604A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.694A pdb=" N LYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.616A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.688A pdb=" N ARG B 516 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.693A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 111 through 120 removed outlier: 4.191A pdb=" N GLY C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 151 through 157 removed outlier: 4.931A pdb=" N LYS C 156 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.736A pdb=" N LEU C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 208 removed outlier: 4.008A pdb=" N VAL C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.542A pdb=" N LYS C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.872A pdb=" N LYS C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 470 through 473 removed outlier: 3.997A pdb=" N MET C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 470 through 473' Processing sheet with id=AA1, first strand: chain 'B' and resid 579 through 581 removed outlier: 3.812A pdb=" N ALA C 355 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.098A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 373 removed outlier: 3.819A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 561 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.939A pdb=" N CYS C 107 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 56 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 53 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 149 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 55 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.550A pdb=" N TYR C 160 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 307 removed outlier: 4.151A pdb=" N TYR C 224 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 467 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 255 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 1554 1.45 - 1.57: 3578 1.57 - 1.69: 92 1.69 - 1.81: 32 Bond restraints: 6913 Sorted by residual: bond pdb=" C3' DA J 1 " pdb=" O3' DA J 1 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C3' DC J -1 " pdb=" O3' DC J -1 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CG LEU B 426 " pdb=" CD1 LEU B 426 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CG PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.05e+00 ... (remaining 6908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 9482 2.52 - 5.04: 92 5.04 - 7.55: 10 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 9586 Sorted by residual: angle pdb=" CA GLU B 508 " pdb=" CB GLU B 508 " pdb=" CG GLU B 508 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 128.89 -12.59 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CB MET C 299 " pdb=" CG MET C 299 " pdb=" SD MET C 299 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.25e+00 angle pdb=" CA ARG C 138 " pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" CA PRO C 273 " pdb=" N PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 112.00 108.37 3.63 1.40e+00 5.10e-01 6.73e+00 ... (remaining 9581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 3813 35.12 - 70.25: 289 70.25 - 105.37: 15 105.37 - 140.50: 1 140.50 - 175.62: 3 Dihedral angle restraints: 4121 sinusoidal: 2018 harmonic: 2103 Sorted by residual: dihedral pdb=" CA PHE B 328 " pdb=" C PHE B 328 " pdb=" N PRO B 329 " pdb=" CA PRO B 329 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL C 463 " pdb=" C VAL C 463 " pdb=" N ASN C 464 " pdb=" CA ASN C 464 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE C 14 " pdb=" C ILE C 14 " pdb=" N PRO C 15 " pdb=" CA PRO C 15 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 4118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 684 0.029 - 0.059: 269 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 17 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1' G I 7 " pdb=" O4' G I 7 " pdb=" C2' G I 7 " pdb=" N9 G I 7 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 407 " pdb=" N ILE C 407 " pdb=" C ILE C 407 " pdb=" CB ILE C 407 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CB ILE C 305 " pdb=" CA ILE C 305 " pdb=" CG1 ILE C 305 " pdb=" CG2 ILE C 305 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1083 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 272 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 273 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 273 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 56 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 57 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U I 5 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 U I 5 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U I 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 5 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I 5 " -0.005 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 43 2.54 - 3.13: 4720 3.13 - 3.72: 10334 3.72 - 4.31: 14501 4.31 - 4.90: 23667 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OP1 A I 1 " pdb="MG MG I 101 " model vdw 1.950 2.170 nonbonded pdb=" OP3 A I 1 " pdb="MG MG I 101 " model vdw 2.001 2.170 nonbonded pdb=" O MET C 473 " pdb="MG MG I 101 " model vdw 2.015 2.170 nonbonded pdb=" O GLN C 281 " pdb=" OG SER C 285 " model vdw 2.225 3.040 nonbonded pdb=" O LEU C 426 " pdb=" OG1 THR C 429 " model vdw 2.233 3.040 ... (remaining 53260 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: 0.590 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.003 0.046 6913 Z= 0.187 Angle : 0.615 12.588 9586 Z= 0.325 Chirality : 0.040 0.147 1086 Planarity : 0.005 0.086 1063 Dihedral : 21.500 175.621 2769 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 33.50 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.32), residues: 718 helix: 1.49 (0.37), residues: 211 sheet: -0.16 (0.44), residues: 160 loop : -1.30 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS B 437 PHE 0.010 0.001 PHE C 158 TYR 0.013 0.001 TYR C 469 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.624 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.9425 time to fit residues: 75.7374 Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133826 restraints weight = 7786.423| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.92 r_work: 0.3690 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6913 Z= 0.165 Angle : 0.557 8.582 9586 Z= 0.295 Chirality : 0.039 0.136 1086 Planarity : 0.005 0.058 1063 Dihedral : 19.474 173.851 1455 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.29 % Allowed : 30.53 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.32), residues: 718 helix: 1.66 (0.36), residues: 224 sheet: 0.12 (0.44), residues: 156 loop : -1.29 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.007 0.001 PHE C 158 TYR 0.009 0.001 TYR C 341 ARG 0.005 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7964 (m-30) cc_final: 0.7754 (m-30) outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.9158 time to fit residues: 81.5742 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.161091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129393 restraints weight = 7970.414| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.96 r_work: 0.3624 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6913 Z= 0.213 Angle : 0.584 8.614 9586 Z= 0.309 Chirality : 0.042 0.198 1086 Planarity : 0.005 0.056 1063 Dihedral : 19.466 174.779 1438 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.62 % Allowed : 31.85 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 718 helix: 1.57 (0.36), residues: 224 sheet: 0.10 (0.43), residues: 157 loop : -1.35 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 166 PHE 0.009 0.001 PHE C 158 TYR 0.015 0.001 TYR C 341 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7959 (m-30) cc_final: 0.7684 (m-30) REVERT: B 528 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7153 (ttt-90) outliers start: 28 outliers final: 9 residues processed: 80 average time/residue: 0.9564 time to fit residues: 81.8766 Evaluate side-chains 67 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 64 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.162514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130818 restraints weight = 7984.109| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.97 r_work: 0.3656 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6913 Z= 0.177 Angle : 0.555 7.097 9586 Z= 0.294 Chirality : 0.040 0.179 1086 Planarity : 0.005 0.053 1063 Dihedral : 19.409 174.903 1437 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.29 % Allowed : 32.51 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.32), residues: 718 helix: 1.71 (0.36), residues: 226 sheet: 0.23 (0.44), residues: 154 loop : -1.33 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS C 166 PHE 0.007 0.001 PHE C 158 TYR 0.011 0.001 TYR C 341 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7924 (m-30) cc_final: 0.7608 (m-30) REVERT: B 528 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7115 (ttt-90) REVERT: C 260 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6899 (p90) outliers start: 26 outliers final: 8 residues processed: 79 average time/residue: 0.9690 time to fit residues: 81.9496 Evaluate side-chains 64 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.160890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129159 restraints weight = 7920.773| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.97 r_work: 0.3646 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6913 Z= 0.203 Angle : 0.568 6.793 9586 Z= 0.302 Chirality : 0.041 0.181 1086 Planarity : 0.005 0.057 1063 Dihedral : 19.425 175.302 1437 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.12 % Allowed : 32.34 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.32), residues: 718 helix: 1.67 (0.36), residues: 226 sheet: 0.18 (0.44), residues: 159 loop : -1.32 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 377 HIS 0.002 0.001 HIS C 306 PHE 0.007 0.001 PHE C 143 TYR 0.015 0.001 TYR C 341 ARG 0.006 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7921 (m-30) cc_final: 0.7560 (m-30) REVERT: B 528 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7161 (ttt-90) REVERT: C 260 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7071 (p90) outliers start: 31 outliers final: 9 residues processed: 86 average time/residue: 0.9824 time to fit residues: 90.1770 Evaluate side-chains 68 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.158803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127043 restraints weight = 7834.265| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.95 r_work: 0.3599 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6913 Z= 0.250 Angle : 0.620 8.592 9586 Z= 0.326 Chirality : 0.043 0.201 1086 Planarity : 0.005 0.060 1063 Dihedral : 19.505 175.349 1437 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.27 % Favored : 93.59 % Rotamer: Outliers : 4.62 % Allowed : 32.67 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 718 helix: 1.37 (0.35), residues: 224 sheet: 0.24 (0.44), residues: 156 loop : -1.41 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 377 HIS 0.004 0.001 HIS C 166 PHE 0.010 0.001 PHE C 143 TYR 0.021 0.002 TYR C 341 ARG 0.007 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7905 (m-30) cc_final: 0.7542 (m-30) REVERT: C 352 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.5820 (tttt) outliers start: 28 outliers final: 14 residues processed: 82 average time/residue: 0.9564 time to fit residues: 83.7438 Evaluate side-chains 77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 0.0060 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.161249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130105 restraints weight = 7836.038| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.93 r_work: 0.3605 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6913 Z= 0.227 Angle : 0.616 7.843 9586 Z= 0.323 Chirality : 0.042 0.186 1086 Planarity : 0.005 0.062 1063 Dihedral : 19.502 175.465 1435 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.46 % Allowed : 33.00 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 718 helix: 1.32 (0.35), residues: 225 sheet: 0.22 (0.44), residues: 161 loop : -1.38 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 306 PHE 0.009 0.001 PHE C 90 TYR 0.017 0.001 TYR C 341 ARG 0.007 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7914 (m-30) cc_final: 0.7565 (m-30) REVERT: B 528 ARG cc_start: 0.7365 (ttp80) cc_final: 0.7110 (ttt-90) REVERT: C 346 ASP cc_start: 0.7878 (m-30) cc_final: 0.7207 (m-30) REVERT: C 352 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.5851 (tttt) outliers start: 27 outliers final: 15 residues processed: 79 average time/residue: 1.0086 time to fit residues: 85.1364 Evaluate side-chains 73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.161116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129554 restraints weight = 7949.427| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.95 r_work: 0.3684 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6913 Z= 0.187 Angle : 0.596 8.153 9586 Z= 0.312 Chirality : 0.041 0.171 1086 Planarity : 0.005 0.062 1063 Dihedral : 19.468 176.037 1435 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.30 % Allowed : 33.83 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 718 helix: 1.49 (0.35), residues: 220 sheet: 0.21 (0.45), residues: 157 loop : -1.27 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS C 306 PHE 0.008 0.001 PHE C 90 TYR 0.011 0.001 TYR C 341 ARG 0.007 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7955 (m-30) cc_final: 0.7610 (m-30) REVERT: B 528 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7074 (ttt-90) REVERT: C 119 ASN cc_start: 0.7419 (p0) cc_final: 0.6878 (m110) REVERT: C 346 ASP cc_start: 0.7847 (m-30) cc_final: 0.7266 (m-30) REVERT: C 352 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.5921 (tttt) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.9958 time to fit residues: 86.1167 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128670 restraints weight = 8041.256| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.00 r_work: 0.3611 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6913 Z= 0.210 Angle : 0.619 10.430 9586 Z= 0.321 Chirality : 0.042 0.164 1086 Planarity : 0.005 0.064 1063 Dihedral : 19.480 176.458 1435 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.14 % Allowed : 34.98 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.32), residues: 718 helix: 1.46 (0.35), residues: 220 sheet: 0.17 (0.44), residues: 157 loop : -1.31 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS C 306 PHE 0.008 0.001 PHE C 90 TYR 0.015 0.001 TYR C 341 ARG 0.008 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7951 (m-30) cc_final: 0.7605 (m-30) REVERT: C 119 ASN cc_start: 0.7458 (p0) cc_final: 0.6895 (m-40) REVERT: C 346 ASP cc_start: 0.7826 (m-30) cc_final: 0.7222 (m-30) REVERT: C 352 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.5944 (tttt) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.9919 time to fit residues: 80.7951 Evaluate side-chains 75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.158442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.127009 restraints weight = 8041.011| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.95 r_work: 0.3581 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6913 Z= 0.311 Angle : 0.676 9.823 9586 Z= 0.350 Chirality : 0.046 0.233 1086 Planarity : 0.006 0.067 1063 Dihedral : 19.634 176.231 1435 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 3.30 % Allowed : 35.15 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.32), residues: 718 helix: 1.18 (0.36), residues: 217 sheet: 0.12 (0.44), residues: 159 loop : -1.49 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 377 HIS 0.003 0.001 HIS C 104 PHE 0.012 0.002 PHE C 143 TYR 0.026 0.002 TYR C 341 ARG 0.008 0.001 ARG C 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7917 (m-30) cc_final: 0.7556 (m-30) REVERT: C 346 ASP cc_start: 0.7899 (m-30) cc_final: 0.7280 (m-30) REVERT: C 352 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.5927 (tttt) outliers start: 20 outliers final: 16 residues processed: 77 average time/residue: 1.1296 time to fit residues: 92.1824 Evaluate side-chains 76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.160170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128741 restraints weight = 7960.332| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.96 r_work: 0.3598 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6913 Z= 0.247 Angle : 0.656 9.684 9586 Z= 0.340 Chirality : 0.043 0.202 1086 Planarity : 0.005 0.065 1063 Dihedral : 19.639 176.115 1435 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 2.81 % Allowed : 35.64 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.32), residues: 718 helix: 1.25 (0.36), residues: 218 sheet: 0.14 (0.44), residues: 159 loop : -1.45 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.009 0.001 PHE C 471 TYR 0.020 0.002 TYR C 341 ARG 0.008 0.001 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.43 seconds wall clock time: 87 minutes 57.96 seconds (5277.96 seconds total)