Starting phenix.real_space_refine on Wed Mar 5 15:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edm_28036/03_2025/8edm_28036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edm_28036/03_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_28036/03_2025/8edm_28036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edm_28036/03_2025/8edm_28036.map" model { file = "/net/cci-nas-00/data/ceres_data/8edm_28036/03_2025/8edm_28036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edm_28036/03_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-5624/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: 2.48, per 1000 atoms: 0.99 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: 0.68 Conformation dependent library (CDL) restraints added in 426.6 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: 0.24 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: 0.61 Time building geometry restraints manager: 0.80 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: 0.820 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.640 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- 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 : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2248 time to fit residues: 9.4639 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 : 0.257 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105893 restraints weight = 8029.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107493 restraints weight = 5210.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108572 restraints weight = 3777.721| |-----------------------------------------------------------------------------| 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 : 0.273 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1653 time to fit residues: 4.7083 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 : 0.268 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 9 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.119604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103109 restraints weight = 8090.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.104723 restraints weight = 5349.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.105474 restraints weight = 3863.112| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3643 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= 0.127 Angle : 0.376 6.023 3499 Z= 0.232 Chirality : 0.038 0.114 442 Planarity : 0.003 0.061 482 Dihedral : 3.194 15.667 449 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 2.71 (0.42), residues: 434 helix: 2.66 (0.28), residues: 305 sheet: None (None), residues: 0 loop : -0.36 (0.65), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B2296 HIS 0.003 0.001 HIS B2661 PHE 0.033 0.002 PHE B2295 TYR 0.008 0.001 TYR B2706 ARG 0.002 0.000 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 : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8029 (ptmt) cc_final: 0.7606 (mttm) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1971 time to fit residues: 5.3624 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 : 0.316 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096127 restraints weight = 8302.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097591 restraints weight = 5405.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.098587 restraints weight = 3949.380| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2537 Z= 0.175 Angle : 0.457 8.445 3499 Z= 0.276 Chirality : 0.040 0.171 442 Planarity : 0.004 0.053 482 Dihedral : 4.133 22.810 449 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 2.40 (0.42), residues: 434 helix: 2.43 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.50 (0.64), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B2296 HIS 0.011 0.002 HIS B2661 PHE 0.016 0.002 PHE B2295 TYR 0.013 0.002 TYR B2706 ARG 0.007 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 24 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.249 Fit side-chains REVERT: A 40 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7744 (mttm) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1642 time to fit residues: 4.3228 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 : 0.268 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.110165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093732 restraints weight = 8363.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095158 restraints weight = 5435.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.096149 restraints weight = 3978.478| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2537 Z= 0.194 Angle : 0.426 6.410 3499 Z= 0.257 Chirality : 0.039 0.108 442 Planarity : 0.004 0.059 482 Dihedral : 3.968 18.931 449 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 2.20 (0.42), residues: 434 helix: 2.32 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.89 (0.65), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B2296 HIS 0.003 0.001 HIS A 38 PHE 0.034 0.002 PHE B2295 TYR 0.009 0.001 TYR B2310 ARG 0.002 0.001 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 21 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.320 Fit side-chains REVERT: A 40 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7707 (mttm) outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.1656 time to fit residues: 4.0162 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain B residue 2270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.111265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.095538 restraints weight = 8405.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.096846 restraints weight = 5527.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097859 restraints weight = 4097.769| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6551 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= 0.123 Angle : 0.369 6.176 3499 Z= 0.225 Chirality : 0.038 0.113 442 Planarity : 0.003 0.059 482 Dihedral : 3.465 16.087 449 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 (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: 2.62 (0.43), residues: 434 helix: 2.74 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B2296 HIS 0.003 0.001 HIS A 38 PHE 0.025 0.002 PHE B2295 TYR 0.006 0.001 TYR B2310 ARG 0.001 0.000 ARG B2387 *********************** 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 19 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.308 Fit side-chains REVERT: A 40 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7689 (mttm) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1730 time to fit residues: 3.9718 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.109354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.093736 restraints weight = 8455.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.095170 restraints weight = 5527.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096044 restraints weight = 4034.678| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6918 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= 0.163 Angle : 0.404 6.286 3499 Z= 0.245 Chirality : 0.038 0.117 442 Planarity : 0.003 0.056 482 Dihedral : 3.752 16.721 449 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.69 % Favored : 96.08 % 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: 2.48 (0.43), residues: 434 helix: 2.58 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.96 (0.65), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2296 HIS 0.004 0.001 HIS B2661 PHE 0.026 0.002 PHE B2295 TYR 0.012 0.002 TYR B2706 ARG 0.002 0.000 ARG B2387 *********************** 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 20 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.266 Fit side-chains REVERT: A 40 LYS cc_start: 0.8357 (ptmt) cc_final: 0.7818 (mttm) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.1687 time to fit residues: 3.6545 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 : 0.289 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.107680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092371 restraints weight = 8463.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.093855 restraints weight = 5531.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094754 restraints weight = 4006.639| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7711 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= 0.159 Angle : 0.408 6.342 3499 Z= 0.248 Chirality : 0.039 0.118 442 Planarity : 0.003 0.056 482 Dihedral : 3.922 17.033 449 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.15 % Favored : 95.62 % Rotamer: Outliers : 4.48 % Allowed : 17.91 % 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: 2.40 (0.43), residues: 434 helix: 2.51 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -1.06 (0.66), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2296 HIS 0.005 0.001 HIS B2661 PHE 0.026 0.002 PHE B2295 TYR 0.007 0.002 TYR B2706 ARG 0.001 0.000 ARG B2387 *********************** 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 21 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.293 Fit side-chains REVERT: A 40 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7754 (mttm) REVERT: A 49 TYR cc_start: 0.7015 (m-80) cc_final: 0.6802 (m-10) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 0.1628 time to fit residues: 3.9377 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 : 0.291 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093094 restraints weight = 8340.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094611 restraints weight = 5375.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095607 restraints weight = 3861.269| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.7882 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= 0.145 Angle : 0.384 6.181 3499 Z= 0.234 Chirality : 0.038 0.115 442 Planarity : 0.003 0.058 482 Dihedral : 3.737 16.661 449 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.46 % Favored : 96.31 % 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: 2.52 (0.44), residues: 434 helix: 2.63 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.08 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2296 HIS 0.005 0.001 HIS B2661 PHE 0.020 0.001 PHE B2295 TYR 0.007 0.001 TYR B2310 ARG 0.001 0.000 ARG B2387 *********************** 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: 1 poor density : 18 time to evaluate : 0.240 Fit side-chains REVERT: A 40 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7703 (mttm) REVERT: A 49 TYR cc_start: 0.7179 (m-80) cc_final: 0.6946 (m-10) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1624 time to fit residues: 3.7194 Evaluate side-chains 17 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.107568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092703 restraints weight = 8346.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.094217 restraints weight = 5405.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.095134 restraints weight = 3892.256| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.8066 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= 0.155 Angle : 0.396 6.130 3499 Z= 0.241 Chirality : 0.038 0.118 442 Planarity : 0.003 0.057 482 Dihedral : 3.762 17.154 449 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 2.47 (0.43), residues: 434 helix: 2.64 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.21 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2296 HIS 0.003 0.001 HIS B2661 PHE 0.022 0.002 PHE B2295 TYR 0.008 0.001 TYR B2310 ARG 0.001 0.000 ARG B2387 ********************** 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 18 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.296 Fit side-chains REVERT: A 40 LYS cc_start: 0.8355 (ptmt) cc_final: 0.7821 (mttm) REVERT: A 49 TYR cc_start: 0.7182 (m-80) cc_final: 0.6937 (m-80) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1454 time to fit residues: 3.3115 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain B residue 2228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.093034 restraints weight = 8379.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094565 restraints weight = 5422.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095489 restraints weight = 3882.931| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.8211 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= 0.140 Angle : 0.380 6.156 3499 Z= 0.232 Chirality : 0.038 0.118 442 Planarity : 0.003 0.058 482 Dihedral : 3.636 17.004 449 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: 2.54 (0.43), residues: 434 helix: 2.82 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.44 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2296 HIS 0.005 0.001 HIS B2661 PHE 0.021 0.002 PHE B2295 TYR 0.008 0.001 TYR B2310 ARG 0.001 0.000 ARG B2387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1062.73 seconds wall clock time: 18 minutes 57.51 seconds (1137.51 seconds total)