Starting phenix.real_space_refine on Fri Aug 22 12:56:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.map" model { file = "/net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edm_28036/08_2025/8edm_28036.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 1 5.16 5 C 1560 2.51 5 N 490 2.21 5 O 458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 551 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 1958 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 846 Unresolved non-hydrogen angles: 1101 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'ARG:plan': 8, 'HIS:plan': 6, 'GLN:plan1': 12, 'GLU:plan': 18, 'ASP:plan': 16, 'TYR:plan': 7, 'ASN:plan1': 17, 'TRP:plan': 2, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 392 Time building chain proxies: 0.93, per 1000 atoms: 0.37 Number of scatterers: 2509 At special positions: 0 Unit cell: (72.8, 72.8, 97.76, 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 1 16.00 O 458 8.00 N 490 7.00 C 1560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 130.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.691A pdb=" N GLU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 51 removed outlier: 4.632A pdb=" N SER A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 72 through 97 removed outlier: 4.121A pdb=" N GLU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 2229 through 2235 Processing helix chain 'B' and resid 2239 through 2260 Processing helix chain 'B' and resid 2262 through 2281 removed outlier: 3.639A pdb=" N SER B2266 " --> pdb=" O ASP B2262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B2268 " --> pdb=" O TYR B2264 " (cutoff:3.500A) Processing helix chain 'B' and resid 2282 through 2284 No H-bonds generated for 'chain 'B' and resid 2282 through 2284' Processing helix chain 'B' and resid 2289 through 2303 removed outlier: 4.031A pdb=" N ALA B2293 " --> pdb=" O PRO B2289 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2334 through 2344 removed outlier: 3.713A pdb=" N ALA B2341 " --> pdb=" O GLU B2337 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B2342 " --> pdb=" O VAL B2338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B2343 " --> pdb=" O PHE B2339 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.725A pdb=" N CYS B2350 " --> pdb=" O LEU B2346 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B2352 " --> pdb=" O TRP B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2374 Processing helix chain 'B' and resid 2374 through 2379 removed outlier: 4.091A pdb=" N ARG B2378 " --> pdb=" O LEU B2374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2381 through 2403 removed outlier: 3.892A pdb=" N VAL B2385 " --> pdb=" O SER B2381 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B2386 " --> pdb=" O PRO B2382 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B2403 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2423 removed outlier: 4.494A pdb=" N TYR B2417 " --> pdb=" O GLN B2413 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B2423 " --> pdb=" O ALA B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2608 removed outlier: 3.742A pdb=" N TYR B2608 " --> pdb=" O THR B2604 " (cutoff:3.500A) Processing helix chain 'B' and resid 2611 through 2629 Processing helix chain 'B' and resid 2632 through 2637 removed outlier: 3.870A pdb=" N VAL B2636 " --> pdb=" O VAL B2632 " (cutoff:3.500A) Processing helix chain 'B' and resid 2640 through 2651 Processing helix chain 'B' and resid 2653 through 2670 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2674 through 2677 Processing helix chain 'B' and resid 2678 through 2684 removed outlier: 4.260A pdb=" N LEU B2682 " --> pdb=" O GLN B2678 " (cutoff:3.500A) Processing helix chain 'B' and resid 2706 through 2721 219 hydrogen bonds defined for protein. 654 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: 0.38 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 928 1.34 - 1.46: 388 1.46 - 1.57: 1219 1.57 - 1.69: 0 1.69 - 1.80: 2 Bond restraints: 2537 Sorted by residual: bond pdb=" C ARG A 5 " pdb=" N PRO A 6 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.51e-02 4.39e+03 2.98e+00 bond pdb=" CA HIS A 4 " pdb=" C HIS A 4 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.08e-02 8.57e+03 8.67e-01 bond pdb=" C GLN B2281 " pdb=" N PRO B2282 " ideal model delta sigma weight residual 1.337 1.329 0.007 9.80e-03 1.04e+04 5.77e-01 bond pdb=" N LEU A 21 " pdb=" CA LEU A 21 " ideal model delta sigma weight residual 1.463 1.456 0.006 8.80e-03 1.29e+04 5.16e-01 bond pdb=" CA ARG A 5 " pdb=" C ARG A 5 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.26e-02 6.30e+03 3.97e-01 ... (remaining 2532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 3398 1.07 - 2.15: 86 2.15 - 3.22: 10 3.22 - 4.29: 4 4.29 - 5.37: 1 Bond angle restraints: 3499 Sorted by residual: angle pdb=" CA ILE B2703 " pdb=" C ILE B2703 " pdb=" N PRO B2704 " ideal model delta sigma weight residual 120.83 118.72 2.11 6.10e-01 2.69e+00 1.19e+01 angle pdb=" C GLN A 20 " pdb=" N LEU A 21 " pdb=" CA LEU A 21 " ideal model delta sigma weight residual 122.26 118.69 3.57 1.10e+00 8.26e-01 1.05e+01 angle pdb=" N ILE B2703 " pdb=" CA ILE B2703 " pdb=" C ILE B2703 " ideal model delta sigma weight residual 112.35 108.93 3.42 1.20e+00 6.94e-01 8.14e+00 angle pdb=" C GLN B2702 " pdb=" N ILE B2703 " pdb=" CA ILE B2703 " ideal model delta sigma weight residual 120.33 122.43 -2.10 8.00e-01 1.56e+00 6.90e+00 angle pdb=" N ARG A 5 " pdb=" CA ARG A 5 " pdb=" C ARG A 5 " ideal model delta sigma weight residual 109.81 115.18 -5.37 2.21e+00 2.05e-01 5.90e+00 ... (remaining 3494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1408 15.37 - 30.73: 48 30.73 - 46.10: 12 46.10 - 61.46: 0 61.46 - 76.83: 1 Dihedral angle restraints: 1469 sinusoidal: 171 harmonic: 1298 Sorted by residual: dihedral pdb=" CG LYS B2236 " pdb=" CD LYS B2236 " pdb=" CE LYS B2236 " pdb=" NZ LYS B2236 " ideal model delta sinusoidal sigma weight residual -60.00 -106.03 46.03 3 1.50e+01 4.44e-03 8.27e+00 dihedral pdb=" CB GLU A 8 " pdb=" CG GLU A 8 " pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sinusoidal sigma weight residual 0.00 76.83 -76.83 1 3.00e+01 1.11e-03 8.24e+00 dihedral pdb=" CA ARG A 5 " pdb=" C ARG A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta harmonic sigma weight residual 180.00 166.25 13.75 0 5.00e+00 4.00e-02 7.56e+00 ... (remaining 1466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 248 0.028 - 0.056: 127 0.056 - 0.084: 53 0.084 - 0.112: 13 0.112 - 0.139: 1 Chirality restraints: 442 Sorted by residual: chirality pdb=" CA ARG A 5 " pdb=" N ARG A 5 " pdb=" C ARG A 5 " pdb=" CB ARG A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA PRO B2634 " pdb=" N PRO B2634 " pdb=" C PRO B2634 " pdb=" CB PRO B2634 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 chirality pdb=" CA PRO B2382 " pdb=" N PRO B2382 " pdb=" C PRO B2382 " pdb=" CB PRO B2382 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.34e-01 ... (remaining 439 not shown) Planarity restraints: 482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 5 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 6 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 6 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 6 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 5 " 0.003 2.00e-02 2.50e+03 5.82e-03 3.39e-01 pdb=" C ARG A 5 " -0.010 2.00e-02 2.50e+03 pdb=" O ARG A 5 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO A 6 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 17 " -0.003 2.00e-02 2.50e+03 5.09e-03 2.60e-01 pdb=" C PHE A 17 " 0.009 2.00e-02 2.50e+03 pdb=" O PHE A 17 " -0.003 2.00e-02 2.50e+03 pdb=" N ASP A 18 " -0.003 2.00e-02 2.50e+03 ... (remaining 479 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 682 2.80 - 3.32: 2599 3.32 - 3.85: 4120 3.85 - 4.37: 3851 4.37 - 4.90: 6893 Nonbonded interactions: 18145 Sorted by model distance: nonbonded pdb=" OD1 ASN B2366 " pdb=" OH TYR B2417 " model vdw 2.271 3.040 nonbonded pdb=" O PHE B2356 " pdb=" OH TYR B2706 " model vdw 2.291 3.040 nonbonded pdb=" O ILE B2234 " pdb=" NZ LYS B2236 " model vdw 2.307 3.120 nonbonded pdb=" O LEU B2657 " pdb=" ND1 HIS B2661 " model vdw 2.329 3.120 nonbonded pdb=" NE1 TRP B2296 " pdb=" O PHE B2339 " model vdw 2.438 3.120 ... (remaining 18140 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.002 0.026 2537 Z= 0.125 Angle : 0.437 5.369 3499 Z= 0.303 Chirality : 0.038 0.139 442 Planarity : 0.003 0.053 482 Dihedral : 9.610 76.830 615 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.44), residues: 434 helix: 2.88 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -0.54 (0.63), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2378 TYR 0.006 0.001 TYR B2721 PHE 0.007 0.001 PHE B2693 TRP 0.006 0.001 TRP B2296 HIS 0.001 0.000 HIS B2379 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2537) covalent geometry : angle 0.43749 ( 3499) hydrogen bonds : bond 0.14758 ( 219) hydrogen bonds : angle 4.82919 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.061 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0649 time to fit residues: 2.7225 Evaluate side-chains 25 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099332 restraints weight = 8189.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100796 restraints weight = 5358.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.101801 restraints weight = 3915.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.102365 restraints weight = 3114.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.102934 restraints weight = 2678.173| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2537 Z= 0.164 Angle : 0.473 6.085 3499 Z= 0.288 Chirality : 0.039 0.108 442 Planarity : 0.004 0.063 482 Dihedral : 4.330 18.784 449 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.49 % Allowed : 17.91 % Favored : 80.60 % 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: 1.80 (0.42), residues: 434 helix: 1.92 (0.28), residues: 310 sheet: None (None), residues: 0 loop : -0.66 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B2387 TYR 0.012 0.003 TYR B2310 PHE 0.014 0.002 PHE B2367 TRP 0.020 0.003 TRP B2296 HIS 0.011 0.003 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2537) covalent geometry : angle 0.47318 ( 3499) hydrogen bonds : bond 0.04501 ( 219) hydrogen bonds : angle 4.13620 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7550 (mttm) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0685 time to fit residues: 1.7849 Evaluate side-chains 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.114404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.098133 restraints weight = 8224.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099629 restraints weight = 5349.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100662 restraints weight = 3884.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101362 restraints weight = 3064.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.101595 restraints weight = 2594.378| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2537 Z= 0.121 Angle : 0.405 6.354 3499 Z= 0.247 Chirality : 0.038 0.122 442 Planarity : 0.003 0.060 482 Dihedral : 3.645 17.779 449 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.99 % Allowed : 17.91 % Favored : 79.10 % 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: 2.31 (0.42), residues: 434 helix: 2.33 (0.28), residues: 305 sheet: None (None), residues: 0 loop : -0.44 (0.66), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 5 TYR 0.009 0.001 TYR B2310 PHE 0.013 0.002 PHE B2339 TRP 0.012 0.001 TRP B2296 HIS 0.002 0.001 HIS B2322 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2537) covalent geometry : angle 0.40534 ( 3499) hydrogen bonds : bond 0.03672 ( 219) hydrogen bonds : angle 3.64143 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.122 Fit side-chains REVERT: A 40 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7738 (mttm) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.0723 time to fit residues: 1.8750 Evaluate side-chains 21 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain B residue 2270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.114445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098602 restraints weight = 8304.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100022 restraints weight = 5409.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.100963 restraints weight = 3945.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.101723 restraints weight = 3163.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.102051 restraints weight = 2662.202| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2537 Z= 0.100 Angle : 0.368 6.321 3499 Z= 0.225 Chirality : 0.038 0.116 442 Planarity : 0.003 0.064 482 Dihedral : 3.447 17.413 449 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.99 % Allowed : 16.42 % Favored : 80.60 % 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: 2.57 (0.43), residues: 434 helix: 2.58 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.70 (0.67), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 5 TYR 0.008 0.001 TYR B2706 PHE 0.013 0.001 PHE B2295 TRP 0.012 0.002 TRP B2296 HIS 0.005 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 2537) covalent geometry : angle 0.36808 ( 3499) hydrogen bonds : bond 0.02997 ( 219) hydrogen bonds : angle 3.42529 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7766 (mttm) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.0588 time to fit residues: 1.5821 Evaluate side-chains 20 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 38 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.109958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.093835 restraints weight = 8311.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095301 restraints weight = 5453.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096135 restraints weight = 3982.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096896 restraints weight = 3237.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.097226 restraints weight = 2760.507| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2537 Z= 0.137 Angle : 0.427 6.703 3499 Z= 0.258 Chirality : 0.038 0.116 442 Planarity : 0.004 0.056 482 Dihedral : 3.960 18.240 449 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.48 % Allowed : 16.42 % Favored : 79.10 % 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: 2.22 (0.43), residues: 434 helix: 2.27 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.83 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 5 TYR 0.012 0.002 TYR B2310 PHE 0.011 0.002 PHE B2367 TRP 0.012 0.002 TRP B2296 HIS 0.007 0.002 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2537) covalent geometry : angle 0.42662 ( 3499) hydrogen bonds : bond 0.04014 ( 219) hydrogen bonds : angle 3.81081 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.099 Fit side-chains REVERT: A 38 HIS cc_start: 0.6255 (OUTLIER) cc_final: 0.5742 (p-80) REVERT: A 40 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7800 (mttm) REVERT: A 55 ILE cc_start: 0.8087 (mt) cc_final: 0.7858 (mm) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.0713 time to fit residues: 1.8595 Evaluate side-chains 22 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 2228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.107738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.092120 restraints weight = 8396.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093563 restraints weight = 5555.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.094572 restraints weight = 4049.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.095119 restraints weight = 3220.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095411 restraints weight = 2759.982| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2537 Z= 0.164 Angle : 0.458 6.345 3499 Z= 0.277 Chirality : 0.040 0.115 442 Planarity : 0.004 0.058 482 Dihedral : 4.241 16.936 449 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.48 % Allowed : 20.90 % Favored : 74.63 % 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: 1.72 (0.42), residues: 434 helix: 1.91 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.06 (0.67), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2387 TYR 0.016 0.002 TYR B2706 PHE 0.011 0.001 PHE B2295 TRP 0.010 0.001 TRP B2296 HIS 0.005 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2537) covalent geometry : angle 0.45782 ( 3499) hydrogen bonds : bond 0.04229 ( 219) hydrogen bonds : angle 3.89320 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.082 Fit side-chains REVERT: A 38 HIS cc_start: 0.6438 (p-80) cc_final: 0.6229 (m90) REVERT: A 40 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7768 (mttm) REVERT: A 55 ILE cc_start: 0.8100 (mt) cc_final: 0.7836 (mm) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.0693 time to fit residues: 1.4642 Evaluate side-chains 20 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain B residue 2270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.088946 restraints weight = 8457.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090347 restraints weight = 5540.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091295 restraints weight = 4067.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091873 restraints weight = 3261.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.092394 restraints weight = 2808.401| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2537 Z= 0.223 Angle : 0.534 6.454 3499 Z= 0.323 Chirality : 0.041 0.114 442 Planarity : 0.004 0.050 482 Dihedral : 5.007 19.329 449 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.48 % Allowed : 20.90 % Favored : 74.63 % 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: 0.98 (0.40), residues: 434 helix: 1.43 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.54 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 5 TYR 0.022 0.003 TYR B2706 PHE 0.017 0.002 PHE A 17 TRP 0.012 0.002 TRP B2296 HIS 0.009 0.002 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 2537) covalent geometry : angle 0.53389 ( 3499) hydrogen bonds : bond 0.05289 ( 219) hydrogen bonds : angle 4.52143 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.077 Fit side-chains REVERT: A 40 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7772 (mttm) REVERT: A 55 ILE cc_start: 0.8203 (mt) cc_final: 0.7907 (mm) outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.0677 time to fit residues: 1.7074 Evaluate side-chains 20 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain B residue 2228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.0470 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092356 restraints weight = 8304.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.093785 restraints weight = 5352.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094742 restraints weight = 3897.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095232 restraints weight = 3109.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095232 restraints weight = 2695.226| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.8142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2537 Z= 0.108 Angle : 0.394 5.919 3499 Z= 0.241 Chirality : 0.038 0.120 442 Planarity : 0.003 0.057 482 Dihedral : 3.894 15.949 449 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % 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: 1.97 (0.43), residues: 434 helix: 2.35 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -1.45 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2248 TYR 0.005 0.001 TYR B2310 PHE 0.027 0.002 PHE A 17 TRP 0.009 0.001 TRP B2296 HIS 0.004 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2537) covalent geometry : angle 0.39375 ( 3499) hydrogen bonds : bond 0.03284 ( 219) hydrogen bonds : angle 3.77737 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.063 Fit side-chains REVERT: A 40 LYS cc_start: 0.8284 (ptmt) cc_final: 0.7685 (mttm) REVERT: A 55 ILE cc_start: 0.8388 (mt) cc_final: 0.8132 (mm) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0805 time to fit residues: 1.6935 Evaluate side-chains 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 10 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.0050 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092424 restraints weight = 8527.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093904 restraints weight = 5468.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094803 restraints weight = 3937.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095584 restraints weight = 3144.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.096037 restraints weight = 2641.854| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.8208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2537 Z= 0.113 Angle : 0.397 5.886 3499 Z= 0.241 Chirality : 0.038 0.121 442 Planarity : 0.003 0.055 482 Dihedral : 3.747 15.136 449 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % 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: 2.14 (0.43), residues: 434 helix: 2.54 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.56 (0.62), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2387 TYR 0.011 0.001 TYR A 49 PHE 0.025 0.002 PHE A 17 TRP 0.011 0.001 TRP B2296 HIS 0.005 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 2537) covalent geometry : angle 0.39734 ( 3499) hydrogen bonds : bond 0.03374 ( 219) hydrogen bonds : angle 3.75294 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.100 Fit side-chains REVERT: A 40 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7714 (mttm) REVERT: A 55 ILE cc_start: 0.8374 (mt) cc_final: 0.8125 (mm) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0781 time to fit residues: 1.5766 Evaluate side-chains 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.093976 restraints weight = 8430.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.095451 restraints weight = 5388.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.096482 restraints weight = 3865.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.096871 restraints weight = 3044.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097543 restraints weight = 2665.555| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2537 Z= 0.095 Angle : 0.371 5.770 3499 Z= 0.225 Chirality : 0.037 0.122 442 Planarity : 0.003 0.058 482 Dihedral : 3.464 14.069 449 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % 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: 2.34 (0.43), residues: 434 helix: 2.67 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.62 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2248 TYR 0.008 0.001 TYR A 49 PHE 0.026 0.001 PHE A 17 TRP 0.009 0.001 TRP B2296 HIS 0.004 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 2537) covalent geometry : angle 0.37128 ( 3499) hydrogen bonds : bond 0.02864 ( 219) hydrogen bonds : angle 3.56404 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.100 Fit side-chains REVERT: A 40 LYS cc_start: 0.8337 (ptmt) cc_final: 0.7759 (mttm) REVERT: A 55 ILE cc_start: 0.8394 (mt) cc_final: 0.8193 (mm) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0681 time to fit residues: 1.3187 Evaluate side-chains 17 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093131 restraints weight = 8356.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.094654 restraints weight = 5418.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095590 restraints weight = 3903.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096181 restraints weight = 3097.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096182 restraints weight = 2642.383| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2537 Z= 0.104 Angle : 0.368 5.311 3499 Z= 0.225 Chirality : 0.037 0.105 442 Planarity : 0.003 0.066 482 Dihedral : 3.480 14.280 449 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 26.87 % Favored : 73.13 % 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: 2.41 (0.43), residues: 434 helix: 2.80 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -1.59 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2343 TYR 0.005 0.001 TYR B2310 PHE 0.024 0.002 PHE A 17 TRP 0.010 0.001 TRP B2296 HIS 0.006 0.001 HIS B2661 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 2537) covalent geometry : angle 0.36784 ( 3499) hydrogen bonds : bond 0.03081 ( 219) hydrogen bonds : angle 3.62488 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 588.93 seconds wall clock time: 10 minutes 50.11 seconds (650.11 seconds total)