Starting phenix.real_space_refine on Wed Mar 12 00:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8in8_35592/03_2025/8in8_35592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8in8_35592/03_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_35592/03_2025/8in8_35592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2025/8in8_35592.map" model { file = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2025/8in8_35592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_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-5624/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: 4.54, per 1000 atoms: 0.68 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: 2.04 Conformation dependent library (CDL) restraints added in 689.3 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: 2.18 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: 2.54 Time building geometry restraints manager: 2.36 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- 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 : 0.610 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.8858 time to fit residues: 71.4011 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 : 0.615 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133756 restraints weight = 7786.489| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.93 r_work: 0.3691 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.683 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7962 (m-30) cc_final: 0.7749 (m-30) outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.8829 time to fit residues: 78.7568 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 : 0.687 ------------------------------------------------------------------------------- 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: 0.1980 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128758 restraints weight = 7973.673| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.97 r_work: 0.3623 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6913 Z= 0.221 Angle : 0.590 8.157 9586 Z= 0.313 Chirality : 0.042 0.215 1086 Planarity : 0.005 0.056 1063 Dihedral : 19.472 174.968 1438 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.95 % Allowed : 31.85 % 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: -0.16 (0.32), residues: 718 helix: 1.54 (0.36), residues: 224 sheet: 0.05 (0.43), residues: 158 loop : -1.35 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 377 HIS 0.004 0.001 HIS C 166 PHE 0.009 0.001 PHE C 158 TYR 0.016 0.001 TYR C 341 ARG 0.006 0.001 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 88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7960 (m-30) cc_final: 0.7704 (m-30) REVERT: B 528 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7166 (ttt-90) outliers start: 30 outliers final: 10 residues processed: 82 average time/residue: 0.9777 time to fit residues: 85.6398 Evaluate side-chains 67 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 52 LEU 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: 4.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 37 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.4460 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.165008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133675 restraints weight = 7964.696| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.96 r_work: 0.3690 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1170 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= 0.157 Angle : 0.543 7.142 9586 Z= 0.288 Chirality : 0.039 0.179 1086 Planarity : 0.004 0.052 1063 Dihedral : 19.389 174.971 1437 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.13 % Allowed : 32.67 % 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: 0.07 (0.32), residues: 718 helix: 1.79 (0.36), residues: 226 sheet: 0.10 (0.44), residues: 161 loop : -1.24 (0.34), residues: 331 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 0.006 0.001 PHE C 158 TYR 0.008 0.001 TYR B 537 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 87 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7925 (m-30) cc_final: 0.7601 (m-30) REVERT: B 528 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7081 (ttt-90) REVERT: C 119 ASN cc_start: 0.7491 (p0) cc_final: 0.6782 (m110) REVERT: C 260 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6947 (p90) outliers start: 25 outliers final: 8 residues processed: 82 average time/residue: 0.9012 time to fit residues: 79.0808 Evaluate side-chains 66 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 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 14 ILE 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.160181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128436 restraints weight = 7933.779| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.96 r_work: 0.3617 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1280 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= 0.228 Angle : 0.586 6.720 9586 Z= 0.311 Chirality : 0.043 0.200 1086 Planarity : 0.005 0.058 1063 Dihedral : 19.443 175.369 1437 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.46 % Allowed : 32.84 % 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: -0.10 (0.32), residues: 718 helix: 1.60 (0.36), residues: 225 sheet: -0.02 (0.43), residues: 166 loop : -1.31 (0.33), residues: 327 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 143 TYR 0.018 0.002 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: 27 poor density : 64 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6350 (tptp) REVERT: B 455 ASP cc_start: 0.7926 (m-30) cc_final: 0.7557 (m-30) REVERT: B 528 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7174 (ttt-90) REVERT: C 260 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7091 (p90) outliers start: 27 outliers final: 9 residues processed: 85 average time/residue: 1.0439 time to fit residues: 95.0537 Evaluate side-chains 72 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS 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: 0.8980 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.165447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134693 restraints weight = 7745.190| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.92 r_work: 0.3663 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1371 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= 0.176 Angle : 0.571 6.560 9586 Z= 0.302 Chirality : 0.040 0.172 1086 Planarity : 0.005 0.058 1063 Dihedral : 19.409 175.414 1437 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.63 % Allowed : 33.99 % Favored : 62.38 % 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: -0.00 (0.32), residues: 718 helix: 1.63 (0.35), residues: 226 sheet: 0.06 (0.43), residues: 166 loop : -1.22 (0.34), residues: 326 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 0.010 0.001 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 85 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7903 (m-30) cc_final: 0.7517 (m-30) REVERT: B 528 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7120 (ttt-90) REVERT: C 119 ASN cc_start: 0.7410 (p0) cc_final: 0.6715 (m110) REVERT: C 346 ASP cc_start: 0.7808 (m-30) cc_final: 0.7158 (m-30) REVERT: C 352 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6071 (tttt) outliers start: 22 outliers final: 11 residues processed: 80 average time/residue: 0.9772 time to fit residues: 83.4418 Evaluate side-chains 73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.158720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127059 restraints weight = 7885.187| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.93 r_work: 0.3640 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1491 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= 0.256 Angle : 0.621 7.822 9586 Z= 0.325 Chirality : 0.043 0.201 1086 Planarity : 0.005 0.063 1063 Dihedral : 19.479 175.672 1435 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.55 % Favored : 93.31 % 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: -0.18 (0.32), residues: 718 helix: 1.39 (0.35), residues: 226 sheet: 0.20 (0.44), residues: 159 loop : -1.38 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 377 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 *********************** 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 89 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7861 (m-30) cc_final: 0.7515 (m-30) REVERT: B 528 ARG cc_start: 0.7423 (ttm170) cc_final: 0.7163 (ttt-90) REVERT: C 346 ASP cc_start: 0.7886 (m-30) cc_final: 0.7213 (m-30) REVERT: C 352 LYS cc_start: 0.6699 (OUTLIER) cc_final: 0.5853 (tttt) outliers start: 27 outliers final: 14 residues processed: 82 average time/residue: 0.9224 time to fit residues: 81.1216 Evaluate side-chains 73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 58 THR 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 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 0.0000 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 overall best weight: 0.3724 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.165339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134231 restraints weight = 7922.755| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.94 r_work: 0.3703 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6913 Z= 0.163 Angle : 0.586 9.599 9586 Z= 0.305 Chirality : 0.040 0.172 1086 Planarity : 0.005 0.061 1063 Dihedral : 19.400 176.133 1435 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.98 % Allowed : 35.31 % 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: 0.12 (0.33), residues: 718 helix: 1.70 (0.35), residues: 226 sheet: 0.30 (0.44), residues: 163 loop : -1.22 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.006 0.001 PHE C 452 TYR 0.007 0.001 TYR B 537 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 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7930 (m-30) cc_final: 0.7547 (m-30) REVERT: C 119 ASN cc_start: 0.7325 (p0) cc_final: 0.6852 (m-40) REVERT: C 346 ASP cc_start: 0.7796 (m-30) cc_final: 0.7257 (m-30) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.9284 time to fit residues: 74.8021 Evaluate side-chains 73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 580 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.162423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130886 restraints weight = 8035.292| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.97 r_work: 0.3654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1637 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= 0.187 Angle : 0.595 7.849 9586 Z= 0.311 Chirality : 0.040 0.170 1086 Planarity : 0.005 0.065 1063 Dihedral : 19.396 176.793 1435 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.48 % Allowed : 35.31 % Favored : 62.21 % 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: 0.15 (0.32), residues: 718 helix: 1.80 (0.35), residues: 220 sheet: 0.34 (0.44), residues: 163 loop : -1.21 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 502 HIS 0.002 0.001 HIS C 306 PHE 0.007 0.001 PHE C 158 TYR 0.011 0.001 TYR C 469 ARG 0.007 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 76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7882 (m-30) cc_final: 0.7493 (m-30) REVERT: B 528 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7120 (ttt-90) REVERT: C 119 ASN cc_start: 0.7390 (p0) cc_final: 0.6882 (m-40) REVERT: C 346 ASP cc_start: 0.7819 (m-30) cc_final: 0.7259 (m-30) REVERT: C 352 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.5935 (tttt) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 1.0534 time to fit residues: 79.8835 Evaluate side-chains 70 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 B residue 580 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.156489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124953 restraints weight = 8079.735| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.96 r_work: 0.3555 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6913 Z= 0.417 Angle : 0.747 8.517 9586 Z= 0.389 Chirality : 0.049 0.282 1086 Planarity : 0.006 0.069 1063 Dihedral : 19.709 176.064 1435 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.24 % Favored : 92.62 % Rotamer: Outliers : 2.81 % Allowed : 35.15 % Favored : 62.05 % 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: -0.60 (0.31), residues: 718 helix: 0.92 (0.35), residues: 223 sheet: 0.17 (0.44), residues: 149 loop : -1.58 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 377 HIS 0.004 0.001 HIS C 104 PHE 0.017 0.002 PHE C 471 TYR 0.034 0.003 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 83 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7870 (m-30) cc_final: 0.7510 (m-30) REVERT: B 528 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7228 (ttt-90) REVERT: C 352 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.5896 (tttt) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 1.0713 time to fit residues: 88.8471 Evaluate side-chains 72 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 58 THR 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 352 LYS Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.160415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129176 restraints weight = 7980.165| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.92 r_work: 0.3639 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6913 Z= 0.188 Angle : 0.630 9.552 9586 Z= 0.329 Chirality : 0.041 0.161 1086 Planarity : 0.005 0.065 1063 Dihedral : 19.580 175.820 1435 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.82 % Allowed : 36.14 % Favored : 62.05 % 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: -0.13 (0.32), residues: 718 helix: 1.47 (0.35), residues: 220 sheet: 0.20 (0.44), residues: 158 loop : -1.31 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 502 HIS 0.004 0.001 HIS C 306 PHE 0.007 0.001 PHE C 452 TYR 0.012 0.001 TYR C 54 ARG 0.007 0.001 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4990.61 seconds wall clock time: 85 minutes 45.42 seconds (5145.42 seconds total)