Starting phenix.real_space_refine on Thu Mar 6 02:01:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcm_51234/03_2025/9gcm_51234.cif" } resolution = 3.1 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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 11 5.16 5 C 2553 2.51 5 N 811 2.21 5 O 1025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1413 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 52} Chain breaks: 1 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1032 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1261 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 760 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 4.90, per 1000 atoms: 1.10 Number of scatterers: 4466 At special positions: 0 Unit cell: (86.87, 89.06, 84.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 66 15.00 O 1025 8.00 N 811 7.00 C 2553 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: 1.10 Conformation dependent library (CDL) restraints added in 380.5 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 53.1% alpha, 12.5% beta 25 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'B' and resid 2 through 13 removed outlier: 4.288A pdb=" N GLU B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 7 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.847A pdb=" N CYS B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.618A pdb=" N VAL B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.609A pdb=" N ARG B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.920A pdb=" N GLY C 17 " --> pdb=" O PRO C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 101 through 113 removed outlier: 4.063A pdb=" N VAL C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 151 removed outlier: 3.802A pdb=" N GLY C 151 " --> pdb=" O LYS C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 151' Processing helix chain 'D' and resid 292 through 332 removed outlier: 3.730A pdb=" N VAL D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 removed outlier: 4.116A pdb=" N LYS D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 384 removed outlier: 3.744A pdb=" N ALA D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 354 " --> pdb=" O HIS D 350 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 3.600A pdb=" N ASP B 121 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B 46 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 125 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 126 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 84 removed outlier: 5.272A pdb=" N ILE C 77 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLU C 98 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG C 79 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE C 96 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ARG C 81 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR C 94 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL C 83 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.078A pdb=" N LYS C 147 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 152 " --> pdb=" O LYS C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 142 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.31 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: 1113 1.33 - 1.45: 1238 1.45 - 1.58: 2176 1.58 - 1.70: 131 1.70 - 1.82: 19 Bond restraints: 4677 Sorted by residual: bond pdb=" CB PRO C 26 " pdb=" CG PRO C 26 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CB LYS D 295 " pdb=" CG LYS D 295 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.07e-01 bond pdb=" CB GLU C 129 " pdb=" CG GLU C 129 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.65e-01 bond pdb=" CB ARG D 314 " pdb=" CG ARG D 314 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CG ARG D 314 " pdb=" CD ARG D 314 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.33e-01 ... (remaining 4672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6460 1.77 - 3.54: 121 3.54 - 5.32: 21 5.32 - 7.09: 9 7.09 - 8.86: 2 Bond angle restraints: 6613 Sorted by residual: angle pdb=" CA PRO C 26 " pdb=" N PRO C 26 " pdb=" CD PRO C 26 " ideal model delta sigma weight residual 112.00 106.80 5.20 1.40e+00 5.10e-01 1.38e+01 angle pdb=" CA LYS D 336 " pdb=" CB LYS D 336 " pdb=" CG LYS D 336 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.32e+00 angle pdb=" CB ARG D 314 " pdb=" CG ARG D 314 " pdb=" CD ARG D 314 " ideal model delta sigma weight residual 111.30 118.10 -6.80 2.30e+00 1.89e-01 8.73e+00 angle pdb=" CB MET D 376 " pdb=" CG MET D 376 " pdb=" SD MET D 376 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" CA LYS D 295 " pdb=" CB LYS D 295 " pdb=" CG LYS D 295 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.16e+00 ... (remaining 6608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 2516 23.08 - 46.16: 301 46.16 - 69.23: 113 69.23 - 92.31: 19 92.31 - 115.39: 2 Dihedral angle restraints: 2951 sinusoidal: 1864 harmonic: 1087 Sorted by residual: dihedral pdb=" O4' U A 22 " pdb=" C1' U A 22 " pdb=" N1 U A 22 " pdb=" C2 U A 22 " ideal model delta sinusoidal sigma weight residual -128.00 -64.15 -63.85 1 1.70e+01 3.46e-03 1.86e+01 dihedral pdb=" O4' G A 55 " pdb=" C1' G A 55 " pdb=" N9 G A 55 " pdb=" C4 G A 55 " ideal model delta sinusoidal sigma weight residual -106.00 -159.65 53.65 1 1.70e+01 3.46e-03 1.35e+01 dihedral pdb=" O4' A A 20 " pdb=" C1' A A 20 " pdb=" N9 A A 20 " pdb=" C4 A A 20 " ideal model delta sinusoidal sigma weight residual -90.00 -29.93 -60.07 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 514 0.024 - 0.048: 151 0.048 - 0.073: 65 0.073 - 0.097: 40 0.097 - 0.121: 13 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA ILE C 97 " pdb=" N ILE C 97 " pdb=" C ILE C 97 " pdb=" CB ILE C 97 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE C 136 " pdb=" N ILE C 136 " pdb=" C ILE C 136 " pdb=" CB ILE C 136 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 780 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 25 " 0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 26 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A 78 " -0.030 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 C A 78 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 78 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C A 78 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C A 78 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 78 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 78 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C A 78 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 78 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 12 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO C 13 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 13 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 13 " 0.026 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 215 2.69 - 3.24: 4546 3.24 - 3.80: 7861 3.80 - 4.35: 10332 4.35 - 4.90: 14833 Nonbonded interactions: 37787 Sorted by model distance: nonbonded pdb=" O2' G A 63 " pdb=" OG SER C 150 " model vdw 2.142 3.040 nonbonded pdb=" O LYS D 308 " pdb=" OG1 THR D 312 " model vdw 2.232 3.040 nonbonded pdb=" N GLU C 102 " pdb=" OE1 GLU C 102 " model vdw 2.237 3.120 nonbonded pdb=" O2' C A 62 " pdb=" OE2 GLU C 149 " model vdw 2.255 3.040 nonbonded pdb=" O LYS C 68 " pdb=" OG SER C 72 " model vdw 2.260 3.040 ... (remaining 37782 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: 5.600 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 4677 Z= 0.234 Angle : 0.651 8.859 6613 Z= 0.332 Chirality : 0.034 0.121 783 Planarity : 0.006 0.086 604 Dihedral : 20.804 115.389 2251 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.23 % Favored : 96.23 % Rotamer: Outliers : 0.93 % Allowed : 25.08 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.45), residues: 371 helix: 0.74 (0.41), residues: 162 sheet: -1.76 (1.03), residues: 21 loop : -0.43 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 32 HIS 0.006 0.002 HIS D 350 PHE 0.010 0.002 PHE C 54 TYR 0.023 0.003 TYR C 39 ARG 0.015 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.2778 time to fit residues: 23.4521 Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.105610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080820 restraints weight = 13489.553| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.26 r_work: 0.3390 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4677 Z= 0.204 Angle : 0.597 7.824 6613 Z= 0.308 Chirality : 0.036 0.203 783 Planarity : 0.005 0.048 604 Dihedral : 20.078 109.969 1462 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.23 % Favored : 96.23 % Rotamer: Outliers : 3.41 % Allowed : 21.36 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.45), residues: 371 helix: 0.87 (0.39), residues: 173 sheet: -2.37 (0.93), residues: 28 loop : -0.06 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 32 HIS 0.010 0.003 HIS D 350 PHE 0.012 0.002 PHE C 123 TYR 0.014 0.002 TYR C 126 ARG 0.007 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8686 (mmm) cc_final: 0.8418 (mmm) REVERT: B 59 GLN cc_start: 0.8517 (mt0) cc_final: 0.8249 (mt0) REVERT: B 120 ARG cc_start: 0.8395 (tpp80) cc_final: 0.8178 (tpp80) REVERT: C 29 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7397 (ttm110) REVERT: D 320 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7941 (tpt90) REVERT: D 352 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6853 (pt) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.2467 time to fit residues: 23.6133 Evaluate side-chains 70 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.105473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081801 restraints weight = 13425.723| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.01 r_work: 0.3441 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4677 Z= 0.199 Angle : 0.572 9.078 6613 Z= 0.291 Chirality : 0.036 0.187 783 Planarity : 0.004 0.037 604 Dihedral : 20.007 108.768 1456 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.96 % Favored : 96.50 % Rotamer: Outliers : 4.95 % Allowed : 21.67 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.45), residues: 371 helix: 1.05 (0.39), residues: 173 sheet: -2.02 (0.94), residues: 28 loop : -0.03 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 89 HIS 0.009 0.002 HIS D 350 PHE 0.009 0.002 PHE C 54 TYR 0.015 0.002 TYR C 39 ARG 0.003 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8842 (mmm) cc_final: 0.8546 (mmm) REVERT: B 39 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7318 (tp40) REVERT: B 59 GLN cc_start: 0.8462 (mt0) cc_final: 0.8040 (mt0) REVERT: B 120 ARG cc_start: 0.8349 (tpp80) cc_final: 0.8140 (mmm-85) REVERT: C 29 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7407 (ttm110) REVERT: D 320 ARG cc_start: 0.8338 (tpt90) cc_final: 0.8056 (tpt90) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.2690 time to fit residues: 27.9389 Evaluate side-chains 78 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.107762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083702 restraints weight = 13496.142| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.24 r_work: 0.3437 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4677 Z= 0.145 Angle : 0.540 10.803 6613 Z= 0.269 Chirality : 0.034 0.185 783 Planarity : 0.004 0.037 604 Dihedral : 19.833 109.768 1456 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.89 % Favored : 97.57 % Rotamer: Outliers : 6.19 % Allowed : 21.36 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.45), residues: 371 helix: 1.31 (0.40), residues: 172 sheet: -1.65 (0.93), residues: 28 loop : 0.11 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 89 HIS 0.008 0.002 HIS D 350 PHE 0.008 0.001 PHE C 123 TYR 0.016 0.002 TYR C 39 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8879 (mmm) cc_final: 0.8549 (mmm) REVERT: B 39 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7526 (tp40) REVERT: B 59 GLN cc_start: 0.8554 (mt0) cc_final: 0.8139 (mt0) REVERT: B 120 ARG cc_start: 0.8465 (tpp80) cc_final: 0.8184 (mmm-85) REVERT: C 29 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7529 (ttm110) REVERT: D 320 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7836 (tpt90) REVERT: D 362 ARG cc_start: 0.6820 (tpt170) cc_final: 0.6078 (mmp80) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.2988 time to fit residues: 34.1572 Evaluate side-chains 83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.105532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081127 restraints weight = 13615.877| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.21 r_work: 0.3391 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4677 Z= 0.216 Angle : 0.592 11.714 6613 Z= 0.297 Chirality : 0.035 0.166 783 Planarity : 0.004 0.034 604 Dihedral : 19.950 107.531 1456 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.31 % Favored : 95.15 % Rotamer: Outliers : 4.64 % Allowed : 23.22 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.45), residues: 371 helix: 1.10 (0.40), residues: 177 sheet: -1.51 (0.96), residues: 28 loop : 0.05 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 32 HIS 0.009 0.002 HIS D 350 PHE 0.009 0.002 PHE C 54 TYR 0.018 0.002 TYR C 39 ARG 0.008 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8918 (mmm) cc_final: 0.8585 (mmm) REVERT: B 39 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7408 (tp40) REVERT: B 59 GLN cc_start: 0.8527 (mt0) cc_final: 0.8042 (mt0) REVERT: C 29 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7624 (ttm110) REVERT: D 358 LEU cc_start: 0.8648 (tp) cc_final: 0.8277 (tp) REVERT: D 362 ARG cc_start: 0.6935 (tpt170) cc_final: 0.6132 (mmp80) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.3895 time to fit residues: 39.7706 Evaluate side-chains 85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.104603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080168 restraints weight = 13365.987| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.19 r_work: 0.3377 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4677 Z= 0.234 Angle : 0.631 12.535 6613 Z= 0.311 Chirality : 0.036 0.162 783 Planarity : 0.004 0.033 604 Dihedral : 20.050 107.974 1456 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.04 % Favored : 95.42 % Rotamer: Outliers : 4.33 % Allowed : 25.08 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.44), residues: 371 helix: 0.89 (0.39), residues: 177 sheet: -1.65 (0.88), residues: 33 loop : 0.01 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 32 HIS 0.010 0.002 HIS D 350 PHE 0.010 0.002 PHE C 54 TYR 0.014 0.002 TYR C 94 ARG 0.009 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8955 (mmm) cc_final: 0.8610 (mmm) REVERT: B 39 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7335 (tp40) REVERT: B 46 CYS cc_start: 0.7590 (m) cc_final: 0.7321 (m) REVERT: B 59 GLN cc_start: 0.8531 (mt0) cc_final: 0.8004 (mt0) REVERT: C 29 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7775 (ttm110) REVERT: C 61 GLN cc_start: 0.8840 (mp10) cc_final: 0.8494 (mp10) REVERT: D 358 LEU cc_start: 0.8641 (tp) cc_final: 0.8304 (tp) REVERT: D 362 ARG cc_start: 0.6903 (tpt170) cc_final: 0.6092 (mmp80) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.2853 time to fit residues: 29.4055 Evaluate side-chains 86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.108537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.084610 restraints weight = 13573.251| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.12 r_work: 0.3509 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4677 Z= 0.152 Angle : 0.597 13.343 6613 Z= 0.293 Chirality : 0.034 0.175 783 Planarity : 0.004 0.033 604 Dihedral : 19.852 109.234 1456 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.96 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 27.55 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.45), residues: 371 helix: 1.03 (0.40), residues: 178 sheet: -1.09 (0.97), residues: 28 loop : 0.06 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 32 HIS 0.009 0.002 HIS D 350 PHE 0.008 0.001 PHE C 54 TYR 0.018 0.002 TYR C 39 ARG 0.003 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8946 (mmm) cc_final: 0.8608 (mmm) REVERT: B 39 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7376 (tp40) REVERT: B 46 CYS cc_start: 0.7423 (m) cc_final: 0.7127 (m) REVERT: B 59 GLN cc_start: 0.8477 (mt0) cc_final: 0.8114 (mt0) REVERT: C 29 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7496 (ttm110) REVERT: C 61 GLN cc_start: 0.8856 (mp10) cc_final: 0.8542 (mp10) REVERT: D 320 ARG cc_start: 0.8188 (tpt90) cc_final: 0.7866 (tpt90) REVERT: D 346 GLU cc_start: 0.7988 (tp30) cc_final: 0.7739 (tp30) REVERT: D 358 LEU cc_start: 0.8647 (tp) cc_final: 0.8288 (tp) REVERT: D 362 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6192 (mmp80) REVERT: D 365 LEU cc_start: 0.9433 (mp) cc_final: 0.9090 (mp) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.3058 time to fit residues: 34.1920 Evaluate side-chains 87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.107326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083021 restraints weight = 13304.928| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.17 r_work: 0.3434 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4677 Z= 0.174 Angle : 0.612 13.359 6613 Z= 0.302 Chirality : 0.034 0.165 783 Planarity : 0.004 0.032 604 Dihedral : 19.830 107.815 1456 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.23 % Favored : 96.23 % Rotamer: Outliers : 2.48 % Allowed : 27.24 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.45), residues: 371 helix: 1.06 (0.40), residues: 178 sheet: -1.03 (0.98), residues: 28 loop : -0.03 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 32 HIS 0.012 0.002 HIS D 350 PHE 0.008 0.001 PHE C 54 TYR 0.020 0.002 TYR C 39 ARG 0.008 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8947 (mmm) cc_final: 0.8596 (mmm) REVERT: B 39 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7473 (tp40) REVERT: B 46 CYS cc_start: 0.7593 (m) cc_final: 0.7331 (m) REVERT: B 59 GLN cc_start: 0.8517 (mt0) cc_final: 0.8077 (mt0) REVERT: B 118 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7451 (mmp80) REVERT: C 29 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7428 (ttm110) REVERT: C 61 GLN cc_start: 0.8862 (mp10) cc_final: 0.8509 (mp10) REVERT: D 330 LYS cc_start: 0.5113 (mmtm) cc_final: 0.4887 (mmtm) REVERT: D 358 LEU cc_start: 0.8676 (tp) cc_final: 0.8302 (tp) REVERT: D 362 ARG cc_start: 0.7007 (tpt170) cc_final: 0.6152 (mmp80) REVERT: D 365 LEU cc_start: 0.9430 (mp) cc_final: 0.9074 (mp) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.2622 time to fit residues: 27.4797 Evaluate side-chains 89 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 75 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.103861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079453 restraints weight = 13826.305| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.10 r_work: 0.3401 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4677 Z= 0.314 Angle : 0.710 12.167 6613 Z= 0.355 Chirality : 0.038 0.140 783 Planarity : 0.004 0.033 604 Dihedral : 20.263 107.776 1456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.85 % Favored : 94.61 % Rotamer: Outliers : 3.10 % Allowed : 26.32 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.44), residues: 371 helix: 0.75 (0.39), residues: 177 sheet: -1.18 (0.97), residues: 28 loop : -0.29 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 32 HIS 0.013 0.003 HIS D 350 PHE 0.012 0.002 PHE C 123 TYR 0.019 0.003 TYR B 115 ARG 0.009 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.9003 (mmm) cc_final: 0.8656 (mmm) REVERT: B 39 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7378 (tp40) REVERT: B 46 CYS cc_start: 0.7603 (m) cc_final: 0.7361 (m) REVERT: B 59 GLN cc_start: 0.8460 (mt0) cc_final: 0.8043 (mt0) REVERT: C 29 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7656 (ttm110) REVERT: D 358 LEU cc_start: 0.8647 (tp) cc_final: 0.8287 (tp) REVERT: D 362 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6226 (mmp80) REVERT: D 365 LEU cc_start: 0.9382 (mp) cc_final: 0.8972 (mp) outliers start: 10 outliers final: 8 residues processed: 83 average time/residue: 0.2631 time to fit residues: 25.4541 Evaluate side-chains 84 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.106581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082660 restraints weight = 13625.448| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.09 r_work: 0.3469 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4677 Z= 0.189 Angle : 0.649 14.140 6613 Z= 0.320 Chirality : 0.035 0.162 783 Planarity : 0.004 0.033 604 Dihedral : 20.032 108.731 1456 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.50 % Favored : 95.96 % Rotamer: Outliers : 2.79 % Allowed : 26.63 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.45), residues: 371 helix: 0.90 (0.39), residues: 178 sheet: -1.05 (0.98), residues: 28 loop : -0.17 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 32 HIS 0.012 0.002 HIS D 350 PHE 0.009 0.001 PHE C 54 TYR 0.020 0.002 TYR B 115 ARG 0.010 0.001 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8990 (mmm) cc_final: 0.8636 (mmm) REVERT: B 39 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7275 (tp40) REVERT: B 46 CYS cc_start: 0.7486 (m) cc_final: 0.7188 (m) REVERT: B 59 GLN cc_start: 0.8464 (mt0) cc_final: 0.7993 (mt0) REVERT: C 29 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7431 (ttm110) REVERT: C 61 GLN cc_start: 0.8854 (mp10) cc_final: 0.8544 (mp10) REVERT: D 358 LEU cc_start: 0.8676 (tp) cc_final: 0.8317 (tp) REVERT: D 362 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6342 (mmp80) REVERT: D 365 LEU cc_start: 0.9412 (mp) cc_final: 0.9063 (mp) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.2378 time to fit residues: 24.2984 Evaluate side-chains 85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.105862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.081914 restraints weight = 13599.285| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.07 r_work: 0.3450 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4677 Z= 0.220 Angle : 0.665 13.850 6613 Z= 0.331 Chirality : 0.036 0.155 783 Planarity : 0.004 0.033 604 Dihedral : 20.041 107.361 1456 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.31 % Favored : 95.15 % Rotamer: Outliers : 2.48 % Allowed : 27.86 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.44), residues: 371 helix: 0.89 (0.39), residues: 178 sheet: -1.02 (1.00), residues: 28 loop : -0.27 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 32 HIS 0.012 0.002 HIS D 350 PHE 0.011 0.001 PHE C 123 TYR 0.022 0.002 TYR C 39 ARG 0.009 0.001 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.20 seconds wall clock time: 69 minutes 54.78 seconds (4194.78 seconds total)