Starting phenix.real_space_refine on Mon Feb 10 21:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edm_28036/02_2025/8edm_28036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edm_28036/02_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_28036/02_2025/8edm_28036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edm_28036/02_2025/8edm_28036.map" model { file = "/net/cci-nas-00/data/ceres_data/8edm_28036/02_2025/8edm_28036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edm_28036/02_2025/8edm_28036.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} 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: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 392 Time building chain proxies: 2.50, per 1000 atoms: 1.00 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: 0.65 Conformation dependent library (CDL) restraints added in 388.6 milliseconds 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: 0.28 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: 0.71 Time building geometry restraints manager: 0.75 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: 0.720 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.710 Find NCS groups from input model: 0.020 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- 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= 0.143 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP B2296 HIS 0.001 0.000 HIS B2379 PHE 0.007 0.001 PHE B2693 TYR 0.006 0.001 TYR B2721 ARG 0.001 0.000 ARG B2378 *********************** 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 : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2203 time to fit residues: 9.2748 Evaluate side-chains 27 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.122756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105934 restraints weight = 8029.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.107477 restraints weight = 5181.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108592 restraints weight = 3781.933| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2627 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= 0.134 Angle : 0.373 5.672 3499 Z= 0.232 Chirality : 0.038 0.107 442 Planarity : 0.004 0.061 482 Dihedral : 3.298 13.729 449 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.43), residues: 434 helix: 2.71 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.39 (0.68), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2296 HIS 0.004 0.001 HIS A 38 PHE 0.009 0.001 PHE B2365 TYR 0.014 0.002 TYR B2706 ARG 0.002 0.001 ARG B2387 *********************** 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 23 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1779 time to fit residues: 4.9843 Evaluate side-chains 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 9 optimal weight: 0.0000 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.103553 restraints weight = 8103.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.105129 restraints weight = 5298.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106215 restraints weight = 3848.175| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2537 Z= 0.121 Angle : 0.374 6.192 3499 Z= 0.228 Chirality : 0.038 0.109 442 Planarity : 0.003 0.058 482 Dihedral : 3.134 15.321 449 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.42), residues: 434 helix: 2.69 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.33 (0.65), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B2296 HIS 0.005 0.001 HIS B2661 PHE 0.036 0.002 PHE B2295 TYR 0.009 0.001 TYR B2706 ARG 0.002 0.001 ARG B2387 *********************** 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 24 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8025 (ptmt) cc_final: 0.7605 (mttm) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1851 time to fit residues: 5.0193 Evaluate side-chains 22 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 34 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.102262 restraints weight = 8222.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103863 restraints weight = 5382.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.104891 restraints weight = 3904.671| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2537 Z= 0.126 Angle : 0.366 5.690 3499 Z= 0.224 Chirality : 0.037 0.136 442 Planarity : 0.004 0.068 482 Dihedral : 3.213 18.658 449 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.43), residues: 434 helix: 2.85 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -0.38 (0.63), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B2296 HIS 0.004 0.001 HIS A 4 PHE 0.015 0.001 PHE B2295 TYR 0.007 0.001 TYR B2310 ARG 0.006 0.001 ARG A 5 *********************** 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 21 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7660 (mttm) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.1624 time to fit residues: 4.1265 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.117109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100613 restraints weight = 8198.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102087 restraints weight = 5355.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.103128 restraints weight = 3932.519| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2537 Z= 0.122 Angle : 0.420 7.141 3499 Z= 0.252 Chirality : 0.038 0.139 442 Planarity : 0.003 0.059 482 Dihedral : 3.267 16.818 449 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.48 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.43), residues: 434 helix: 2.71 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -0.45 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2296 HIS 0.005 0.001 HIS A 4 PHE 0.015 0.001 PHE B2295 TYR 0.006 0.001 TYR B2706 ARG 0.002 0.000 ARG B2387 *********************** 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 24 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7737 (mttm) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1644 time to fit residues: 4.4856 Evaluate side-chains 21 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B2661 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.114944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.098796 restraints weight = 8350.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.100233 restraints weight = 5484.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.101218 restraints weight = 4006.790| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2537 Z= 0.138 Angle : 0.399 5.985 3499 Z= 0.242 Chirality : 0.038 0.129 442 Planarity : 0.003 0.059 482 Dihedral : 3.296 15.359 449 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.97 % Allowed : 16.42 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.43), residues: 434 helix: 2.65 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -0.50 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2296 HIS 0.006 0.001 HIS A 4 PHE 0.036 0.002 PHE B2295 TYR 0.007 0.001 TYR B2310 ARG 0.003 0.001 ARG A 5 *********************** 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 24 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 4 HIS cc_start: 0.6314 (OUTLIER) cc_final: 0.5720 (p-80) REVERT: A 40 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7707 (mttm) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.1968 time to fit residues: 4.9916 Evaluate side-chains 22 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 2270 ILE Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.114982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099060 restraints weight = 8389.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.100550 restraints weight = 5506.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.101571 restraints weight = 4016.218| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2537 Z= 0.122 Angle : 0.402 5.597 3499 Z= 0.244 Chirality : 0.038 0.138 442 Planarity : 0.003 0.060 482 Dihedral : 3.185 15.133 449 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.43), residues: 434 helix: 2.71 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.54 (0.64), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2296 HIS 0.008 0.001 HIS A 4 PHE 0.024 0.001 PHE B2295 TYR 0.007 0.001 TYR B2310 ARG 0.007 0.001 ARG A 5 *********************** 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 : 0.305 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7710 (mttm) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.1996 time to fit residues: 4.8713 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.097542 restraints weight = 8478.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099074 restraints weight = 5486.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.100137 restraints weight = 3966.934| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2537 Z= 0.125 Angle : 0.390 6.253 3499 Z= 0.237 Chirality : 0.038 0.128 442 Planarity : 0.003 0.063 482 Dihedral : 3.119 14.740 449 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.43), residues: 434 helix: 2.80 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.67 (0.65), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.010 0.002 HIS A 4 PHE 0.024 0.001 PHE B2295 TYR 0.008 0.001 TYR B2310 ARG 0.005 0.001 ARG A 5 *********************** 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 : 0.306 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5457 (p-80) REVERT: A 40 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7692 (mttm) REVERT: A 92 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7508 (ttpt) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.2106 time to fit residues: 4.6414 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.107996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091866 restraints weight = 8359.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093247 restraints weight = 5477.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094155 restraints weight = 4045.704| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2537 Z= 0.240 Angle : 0.512 6.345 3499 Z= 0.308 Chirality : 0.040 0.107 442 Planarity : 0.005 0.075 482 Dihedral : 4.240 17.222 449 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.99 % Allowed : 19.40 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.42), residues: 434 helix: 2.28 (0.28), residues: 312 sheet: None (None), residues: 0 loop : -0.87 (0.64), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B2296 HIS 0.008 0.002 HIS B2661 PHE 0.027 0.002 PHE B2295 TYR 0.010 0.002 TYR B2310 ARG 0.010 0.001 ARG A 5 *********************** 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 19 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7761 (mttm) REVERT: A 92 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7533 (ttpt) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.1843 time to fit residues: 4.2764 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090177 restraints weight = 8387.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091574 restraints weight = 5477.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.092544 restraints weight = 4019.228| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2537 Z= 0.278 Angle : 0.546 7.772 3499 Z= 0.328 Chirality : 0.042 0.165 442 Planarity : 0.004 0.058 482 Dihedral : 4.758 18.239 449 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.49 % Allowed : 22.39 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.41), residues: 434 helix: 1.60 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.35 (0.63), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.007 0.002 HIS B2661 PHE 0.024 0.003 PHE B2295 TYR 0.009 0.002 TYR B2310 ARG 0.012 0.002 ARG A 5 ********************** 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 19 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8292 (ptmt) cc_final: 0.7745 (mttm) REVERT: A 49 TYR cc_start: 0.7187 (m-80) cc_final: 0.6879 (m-80) REVERT: A 92 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7419 (ttpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.2101 time to fit residues: 4.6595 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2665 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.108608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093527 restraints weight = 8295.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095046 restraints weight = 5337.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096077 restraints weight = 3835.259| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2537 Z= 0.127 Angle : 0.415 5.910 3499 Z= 0.251 Chirality : 0.038 0.114 442 Planarity : 0.004 0.053 482 Dihedral : 3.692 14.612 449 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.49 % Allowed : 20.90 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 434 helix: 2.57 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.34 (0.63), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.002 0.001 HIS A 4 PHE 0.021 0.001 PHE B2295 TYR 0.006 0.001 TYR B2310 ARG 0.016 0.002 ARG A 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1046.04 seconds wall clock time: 19 minutes 12.58 seconds (1152.58 seconds total)