Starting phenix.real_space_refine on Wed Sep 17 04:21:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5w_19752/09_2025/8s5w_19752.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2662 2.51 5 N 626 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4009 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3037 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.19, per 1000 atoms: 0.30 Number of scatterers: 4009 At special positions: 0 Unit cell: (100.43, 79.68, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 700 8.00 N 626 7.00 C 2662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 107.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 61.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.651A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.383A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.600A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 removed outlier: 4.204A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.622A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.745A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 removed outlier: 3.707A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 187 removed outlier: 3.647A pdb=" N ASN A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 removed outlier: 3.655A pdb=" N SER A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.539A pdb=" N TRP A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 315 through 337 removed outlier: 3.601A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.571A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.671A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.815A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 456 removed outlier: 4.016A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.605A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.376A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.376A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.040A pdb=" N ARG B 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 592 1.27 - 1.41: 1172 1.41 - 1.54: 2297 1.54 - 1.68: 27 1.68 - 1.81: 36 Bond restraints: 4124 Sorted by residual: bond pdb=" CAR 2TA A 601 " pdb=" CAS 2TA A 601 " ideal model delta sigma weight residual 1.543 1.255 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" CAO 2TA A 601 " pdb=" NAP 2TA A 601 " ideal model delta sigma weight residual 1.444 1.194 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" CAT 2TA A 601 " pdb=" NAP 2TA A 601 " ideal model delta sigma weight residual 1.456 1.279 0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" C ARG A 277 " pdb=" O ARG A 277 " ideal model delta sigma weight residual 1.237 1.136 0.100 1.16e-02 7.43e+03 7.48e+01 bond pdb=" C2 2TA A 601 " pdb=" N1 2TA A 601 " ideal model delta sigma weight residual 1.322 1.482 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 4119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 5578 3.46 - 6.93: 43 6.93 - 10.39: 2 10.39 - 13.86: 1 13.86 - 17.32: 2 Bond angle restraints: 5626 Sorted by residual: angle pdb=" N VAL A 77 " pdb=" CA VAL A 77 " pdb=" C VAL A 77 " ideal model delta sigma weight residual 110.05 101.20 8.85 1.09e+00 8.42e-01 6.59e+01 angle pdb=" OBJ 2TA A 601 " pdb=" SBD 2TA A 601 " pdb=" OBK 2TA A 601 " ideal model delta sigma weight residual 118.13 100.81 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" CA LEU A 190 " pdb=" C LEU A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 118.23 123.02 -4.79 9.20e-01 1.18e+00 2.72e+01 angle pdb=" C2 2TA A 601 " pdb=" NAF 2TA A 601 " pdb=" CAG 2TA A 601 " ideal model delta sigma weight residual 131.32 116.30 15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" CA VAL A 77 " pdb=" C VAL A 77 " pdb=" O VAL A 77 " ideal model delta sigma weight residual 121.98 116.24 5.74 1.21e+00 6.83e-01 2.25e+01 ... (remaining 5621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 2228 29.44 - 58.89: 103 58.89 - 88.33: 9 88.33 - 117.77: 3 117.77 - 147.22: 2 Dihedral angle restraints: 2345 sinusoidal: 873 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 155.56 -62.56 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CAG 2TA A 601 " pdb=" C2 2TA A 601 " pdb=" NAF 2TA A 601 " pdb=" N1 2TA A 601 " ideal model delta sinusoidal sigma weight residual -0.72 -147.94 147.22 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" CAI 2TA A 601 " pdb=" CAJ 2TA A 601 " pdb=" OAM 2TA A 601 " pdb=" CAN 2TA A 601 " ideal model delta sinusoidal sigma weight residual -1.36 129.06 -130.42 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 2342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 499 0.048 - 0.096: 105 0.096 - 0.144: 22 0.144 - 0.192: 3 0.192 - 0.240: 1 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU A 190 " pdb=" N LEU A 190 " pdb=" C LEU A 190 " pdb=" CB LEU A 190 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA LYS B 87 " pdb=" N LYS B 87 " pdb=" C LYS B 87 " pdb=" CB LYS B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 627 not shown) Planarity restraints: 683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 80 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 80 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 80 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 81 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 190 " 0.007 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU A 190 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 190 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO A 191 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 13 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO B 14 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.017 5.00e-02 4.00e+02 ... (remaining 680 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1339 2.83 - 3.35: 3715 3.35 - 3.87: 6532 3.87 - 4.38: 8047 4.38 - 4.90: 13737 Nonbonded interactions: 33370 Sorted by model distance: nonbonded pdb=" O SER A 89 " pdb=" OG1 THR A 93 " model vdw 2.313 3.040 nonbonded pdb=" N VAL A 77 " pdb=" O VAL A 77 " model vdw 2.422 2.496 nonbonded pdb=" N ASN A 340 " pdb=" OD1 ASN A 340 " model vdw 2.428 3.120 nonbonded pdb=" O ASP B 73 " pdb=" OD1 ASP B 73 " model vdw 2.432 3.040 nonbonded pdb=" NAP 2TA A 601 " pdb=" OAM 2TA A 601 " model vdw 2.452 2.496 ... (remaining 33365 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.750 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.012 0.288 4125 Z= 0.633 Angle : 0.836 17.323 5628 Z= 0.478 Chirality : 0.043 0.240 630 Planarity : 0.004 0.030 683 Dihedral : 17.300 147.216 1406 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.24 % Allowed : 19.48 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.36), residues: 496 helix: -1.25 (0.29), residues: 275 sheet: -1.31 (0.86), residues: 43 loop : -0.91 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 109 TYR 0.013 0.001 TYR A 336 PHE 0.007 0.001 PHE A 439 TRP 0.005 0.001 TRP B 110 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.01236 ( 4124) covalent geometry : angle 0.83570 ( 5626) SS BOND : bond 0.00698 ( 1) SS BOND : angle 1.15500 ( 2) hydrogen bonds : bond 0.25401 ( 239) hydrogen bonds : angle 8.95753 ( 729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.091 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0768 time to fit residues: 5.7072 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0670 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.155150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.138536 restraints weight = 4923.728| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.49 r_work: 0.3352 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4125 Z= 0.164 Angle : 0.594 6.532 5628 Z= 0.308 Chirality : 0.042 0.137 630 Planarity : 0.005 0.037 683 Dihedral : 11.445 152.987 571 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.04 % Allowed : 17.34 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.37), residues: 496 helix: 0.48 (0.31), residues: 293 sheet: -0.72 (0.83), residues: 45 loop : -0.94 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.008 0.001 TYR A 336 PHE 0.012 0.002 PHE A 292 TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4124) covalent geometry : angle 0.59381 ( 5626) SS BOND : bond 0.00781 ( 1) SS BOND : angle 1.41407 ( 2) hydrogen bonds : bond 0.05108 ( 239) hydrogen bonds : angle 4.48810 ( 729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: B 52 SER cc_start: 0.8366 (m) cc_final: 0.8092 (t) REVERT: A 347 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7153 (mt) REVERT: A 385 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8524 (tt) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.0608 time to fit residues: 5.6734 Evaluate side-chains 73 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.0060 chunk 2 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.158810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142296 restraints weight = 4930.275| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.48 r_work: 0.3407 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4125 Z= 0.116 Angle : 0.499 5.769 5628 Z= 0.259 Chirality : 0.040 0.134 630 Planarity : 0.004 0.037 683 Dihedral : 10.793 149.744 568 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.33 % Allowed : 19.48 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.38), residues: 496 helix: 1.21 (0.32), residues: 292 sheet: -0.21 (0.82), residues: 45 loop : -0.81 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.014 0.001 TYR A 336 PHE 0.016 0.001 PHE A 439 TRP 0.016 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4124) covalent geometry : angle 0.49903 ( 5626) SS BOND : bond 0.00424 ( 1) SS BOND : angle 0.97988 ( 2) hydrogen bonds : bond 0.04100 ( 239) hydrogen bonds : angle 3.95673 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.147 Fit side-chains REVERT: B 52 SER cc_start: 0.8285 (m) cc_final: 0.8083 (t) REVERT: A 137 GLN cc_start: 0.7335 (pm20) cc_final: 0.6814 (mm-40) REVERT: A 278 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7657 (tp) REVERT: A 347 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7208 (mt) REVERT: A 385 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8527 (tt) outliers start: 14 outliers final: 5 residues processed: 67 average time/residue: 0.0523 time to fit residues: 4.7973 Evaluate side-chains 64 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.138373 restraints weight = 4912.756| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.45 r_work: 0.3381 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4125 Z= 0.149 Angle : 0.547 7.033 5628 Z= 0.279 Chirality : 0.041 0.149 630 Planarity : 0.004 0.036 683 Dihedral : 11.004 149.956 568 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.75 % Allowed : 18.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.38), residues: 496 helix: 1.38 (0.31), residues: 293 sheet: -0.18 (0.77), residues: 51 loop : -0.84 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.009 0.001 TYR A 336 PHE 0.015 0.002 PHE A 439 TRP 0.017 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4124) covalent geometry : angle 0.54638 ( 5626) SS BOND : bond 0.00747 ( 1) SS BOND : angle 1.44417 ( 2) hydrogen bonds : bond 0.04390 ( 239) hydrogen bonds : angle 3.97759 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.154 Fit side-chains REVERT: B 52 SER cc_start: 0.8291 (m) cc_final: 0.8072 (t) REVERT: A 194 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6697 (mptt) REVERT: A 385 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8624 (tt) outliers start: 20 outliers final: 12 residues processed: 72 average time/residue: 0.0570 time to fit residues: 5.4520 Evaluate side-chains 72 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.152335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135700 restraints weight = 4950.446| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.49 r_work: 0.3350 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4125 Z= 0.174 Angle : 0.578 9.639 5628 Z= 0.294 Chirality : 0.042 0.153 630 Planarity : 0.004 0.039 683 Dihedral : 11.221 150.244 568 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.94 % Allowed : 17.34 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.38), residues: 496 helix: 1.45 (0.31), residues: 293 sheet: -0.12 (0.76), residues: 51 loop : -1.02 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.010 0.001 TYR B 112 PHE 0.015 0.002 PHE A 439 TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4124) covalent geometry : angle 0.57737 ( 5626) SS BOND : bond 0.00882 ( 1) SS BOND : angle 1.70696 ( 2) hydrogen bonds : bond 0.04633 ( 239) hydrogen bonds : angle 4.05143 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.122 Fit side-chains REVERT: B 12 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6223 (m) REVERT: A 194 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6674 (mptt) REVERT: A 385 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8642 (tt) outliers start: 25 outliers final: 19 residues processed: 72 average time/residue: 0.0564 time to fit residues: 5.4131 Evaluate side-chains 78 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.138128 restraints weight = 5010.398| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.50 r_work: 0.3381 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4125 Z= 0.145 Angle : 0.546 9.592 5628 Z= 0.277 Chirality : 0.041 0.146 630 Planarity : 0.004 0.042 683 Dihedral : 11.124 149.608 568 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.51 % Allowed : 19.48 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.38), residues: 496 helix: 1.63 (0.31), residues: 293 sheet: 0.02 (0.77), residues: 45 loop : -1.04 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.007 0.001 TYR A 336 PHE 0.013 0.001 PHE A 439 TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4124) covalent geometry : angle 0.54580 ( 5626) SS BOND : bond 0.00766 ( 1) SS BOND : angle 1.52323 ( 2) hydrogen bonds : bond 0.04242 ( 239) hydrogen bonds : angle 3.90359 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.120 Fit side-chains REVERT: A 194 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6632 (mptt) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.0601 time to fit residues: 5.5140 Evaluate side-chains 70 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.154186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137600 restraints weight = 5039.758| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.50 r_work: 0.3336 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4125 Z= 0.151 Angle : 0.550 8.102 5628 Z= 0.279 Chirality : 0.041 0.147 630 Planarity : 0.004 0.043 683 Dihedral : 11.186 149.739 568 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.99 % Allowed : 19.48 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.38), residues: 496 helix: 1.69 (0.31), residues: 293 sheet: 0.03 (0.75), residues: 50 loop : -1.05 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.008 0.001 TYR B 112 PHE 0.013 0.001 PHE A 439 TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4124) covalent geometry : angle 0.54900 ( 5626) SS BOND : bond 0.00799 ( 1) SS BOND : angle 1.57583 ( 2) hydrogen bonds : bond 0.04310 ( 239) hydrogen bonds : angle 3.91762 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.146 Fit side-chains REVERT: A 27 MET cc_start: 0.9096 (mmm) cc_final: 0.8860 (mmm) REVERT: A 194 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6690 (mptt) outliers start: 21 outliers final: 16 residues processed: 70 average time/residue: 0.0558 time to fit residues: 5.2436 Evaluate side-chains 74 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.137592 restraints weight = 4938.584| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.48 r_work: 0.3340 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4125 Z= 0.149 Angle : 0.538 6.319 5628 Z= 0.276 Chirality : 0.041 0.147 630 Planarity : 0.004 0.045 683 Dihedral : 11.193 149.550 568 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.23 % Allowed : 19.95 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.39), residues: 496 helix: 1.79 (0.31), residues: 293 sheet: -0.36 (0.70), residues: 57 loop : -0.96 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.008 0.001 TYR B 112 PHE 0.013 0.001 PHE A 439 TRP 0.018 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4124) covalent geometry : angle 0.53752 ( 5626) SS BOND : bond 0.00796 ( 1) SS BOND : angle 1.57981 ( 2) hydrogen bonds : bond 0.04275 ( 239) hydrogen bonds : angle 3.88144 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.174 Fit side-chains REVERT: A 27 MET cc_start: 0.9095 (mmm) cc_final: 0.8863 (mmm) REVERT: A 194 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6710 (mptt) outliers start: 22 outliers final: 18 residues processed: 71 average time/residue: 0.0585 time to fit residues: 5.4915 Evaluate side-chains 76 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.154279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137808 restraints weight = 5021.138| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.48 r_work: 0.3334 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4125 Z= 0.150 Angle : 0.536 5.521 5628 Z= 0.276 Chirality : 0.041 0.147 630 Planarity : 0.004 0.045 683 Dihedral : 11.216 149.452 568 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.70 % Allowed : 19.48 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.39), residues: 496 helix: 1.82 (0.31), residues: 293 sheet: -0.31 (0.72), residues: 56 loop : -0.99 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.009 0.001 TYR B 112 PHE 0.013 0.001 PHE A 439 TRP 0.018 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4124) covalent geometry : angle 0.53501 ( 5626) SS BOND : bond 0.00821 ( 1) SS BOND : angle 1.63244 ( 2) hydrogen bonds : bond 0.04285 ( 239) hydrogen bonds : angle 3.88117 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.126 Fit side-chains REVERT: A 27 MET cc_start: 0.9104 (mmm) cc_final: 0.8869 (mmm) REVERT: A 194 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6687 (mptt) outliers start: 24 outliers final: 17 residues processed: 71 average time/residue: 0.0554 time to fit residues: 5.2861 Evaluate side-chains 75 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.150353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.133813 restraints weight = 5010.187| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.47 r_work: 0.3316 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4125 Z= 0.217 Angle : 0.602 6.271 5628 Z= 0.312 Chirality : 0.045 0.158 630 Planarity : 0.005 0.046 683 Dihedral : 11.492 150.282 568 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.51 % Allowed : 20.67 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.38), residues: 496 helix: 1.60 (0.31), residues: 293 sheet: -0.38 (0.72), residues: 56 loop : -1.18 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.013 0.002 TYR B 112 PHE 0.014 0.002 PHE A 439 TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 4124) covalent geometry : angle 0.60089 ( 5626) SS BOND : bond 0.01146 ( 1) SS BOND : angle 2.14765 ( 2) hydrogen bonds : bond 0.04946 ( 239) hydrogen bonds : angle 4.11247 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.151 Fit side-chains REVERT: A 194 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6869 (mptt) outliers start: 19 outliers final: 17 residues processed: 68 average time/residue: 0.0530 time to fit residues: 4.8523 Evaluate side-chains 73 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.152704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.136220 restraints weight = 5033.476| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.47 r_work: 0.3353 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4125 Z= 0.155 Angle : 0.540 5.540 5628 Z= 0.281 Chirality : 0.042 0.151 630 Planarity : 0.004 0.045 683 Dihedral : 11.311 149.494 568 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.23 % Allowed : 19.71 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.38), residues: 496 helix: 1.73 (0.31), residues: 293 sheet: -0.32 (0.73), residues: 51 loop : -1.15 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.010 0.001 TYR B 112 PHE 0.012 0.001 PHE A 439 TRP 0.019 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4124) covalent geometry : angle 0.53936 ( 5626) SS BOND : bond 0.00869 ( 1) SS BOND : angle 1.66536 ( 2) hydrogen bonds : bond 0.04380 ( 239) hydrogen bonds : angle 3.96166 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.53 seconds wall clock time: 22 minutes 33.61 seconds (1353.61 seconds total)