Starting phenix.real_space_refine on Thu Dec 7 16:29:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_28036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_28036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_28036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_28036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edm_28036/12_2023/8edm_28036.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.01, per 1000 atoms: 0.80 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 612.5 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: 0.62 Time building geometry restraints manager: 1.18 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: 100.92 - 107.54: 48 107.54 - 114.17: 1433 114.17 - 120.79: 1219 120.79 - 127.42: 785 127.42 - 134.04: 14 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 2.440 nonbonded pdb=" O PHE B2356 " pdb=" OH TYR B2706 " model vdw 2.291 2.440 nonbonded pdb=" O ILE B2234 " pdb=" NZ LYS B2236 " model vdw 2.307 2.520 nonbonded pdb=" O LEU B2657 " pdb=" ND1 HIS B2661 " model vdw 2.329 2.520 nonbonded pdb=" NE1 TRP B2296 " pdb=" O PHE B2339 " model vdw 2.438 2.520 ... (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 ========== 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.670 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2364 time to fit residues: 9.9393 Evaluate side-chains 27 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3666 ------------------------------------------------------------------------------- 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: 0.0670 chunk 32 optimal weight: 0.0870 chunk 18 optimal weight: 0.0970 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2537 Z= 0.105 Angle : 0.356 5.227 3499 Z= 0.217 Chirality : 0.037 0.101 442 Planarity : 0.003 0.062 482 Dihedral : 3.176 15.762 449 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: 2.82 (0.43), residues: 434 helix: 2.77 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.43 (0.68), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B2296 HIS 0.002 0.001 HIS A 38 PHE 0.013 0.001 PHE B2365 TYR 0.013 0.002 TYR B2310 ARG 0.003 0.001 ARG A 5 *********************** 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 25 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1533 time to fit residues: 4.7171 Evaluate side-chains 22 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2537 Z= 0.127 Angle : 0.378 5.831 3499 Z= 0.234 Chirality : 0.038 0.111 442 Planarity : 0.003 0.056 482 Dihedral : 3.242 14.767 449 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 2.68 (0.42), residues: 434 helix: 2.66 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -0.44 (0.64), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B2296 HIS 0.010 0.002 HIS B2661 PHE 0.008 0.001 PHE B2367 TYR 0.008 0.001 TYR B2310 ARG 0.003 0.001 ARG A 5 *********************** 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 25 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.1701 time to fit residues: 4.8248 Evaluate side-chains 22 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0316 time to fit residues: 0.4039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 2537 Z= 0.157 Angle : 0.416 5.154 3499 Z= 0.251 Chirality : 0.038 0.169 442 Planarity : 0.003 0.051 482 Dihedral : 3.638 21.032 449 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.49 % Allowed : 14.93 % Favored : 83.58 % 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: 2.63 (0.42), residues: 434 helix: 2.63 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -0.53 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B2296 HIS 0.006 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 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 22 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.298 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1709 time to fit residues: 4.4838 Evaluate side-chains 20 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0288 time to fit residues: 0.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2537 Z= 0.122 Angle : 0.370 5.824 3499 Z= 0.223 Chirality : 0.037 0.102 442 Planarity : 0.003 0.054 482 Dihedral : 3.391 16.070 449 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.77 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: 2.83 (0.43), residues: 434 helix: 2.76 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -0.46 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2296 HIS 0.003 0.001 HIS B2661 PHE 0.018 0.001 PHE B2295 TYR 0.007 0.001 TYR B2310 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 fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.283 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1577 time to fit residues: 4.3787 Evaluate side-chains 22 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0299 time to fit residues: 0.4966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 2537 Z= 0.090 Angle : 0.350 5.091 3499 Z= 0.214 Chirality : 0.037 0.115 442 Planarity : 0.003 0.054 482 Dihedral : 3.180 15.720 449 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % 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: 2.89 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -0.58 (0.63), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2296 HIS 0.006 0.001 HIS A 38 PHE 0.017 0.001 PHE B2295 TYR 0.007 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 21 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.290 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1564 time to fit residues: 4.1743 Evaluate side-chains 19 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2537 Z= 0.125 Angle : 0.362 4.500 3499 Z= 0.223 Chirality : 0.037 0.105 442 Planarity : 0.003 0.061 482 Dihedral : 3.470 15.943 449 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 20.90 % 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: 2.82 (0.43), residues: 434 helix: 2.78 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.68 (0.66), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B2296 HIS 0.006 0.002 HIS A 4 PHE 0.015 0.002 PHE B2295 TYR 0.006 0.001 TYR B2310 ARG 0.002 0.000 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 18 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1935 time to fit residues: 4.3827 Evaluate side-chains 17 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2537 Z= 0.167 Angle : 0.405 6.549 3499 Z= 0.248 Chirality : 0.039 0.113 442 Planarity : 0.003 0.056 482 Dihedral : 3.822 17.930 449 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 19.40 % 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: 2.56 (0.43), residues: 434 helix: 2.54 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.79 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B2296 HIS 0.011 0.002 HIS A 38 PHE 0.015 0.002 PHE B2295 TYR 0.009 0.001 TYR B2310 ARG 0.002 0.001 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 17 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1481 time to fit residues: 3.3313 Evaluate side-chains 17 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2537 Z= 0.104 Angle : 0.342 4.889 3499 Z= 0.210 Chirality : 0.037 0.103 442 Planarity : 0.003 0.062 482 Dihedral : 3.345 13.581 449 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 17.91 % 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: 2.82 (0.43), residues: 434 helix: 2.85 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.88 (0.63), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2296 HIS 0.003 0.001 HIS A 38 PHE 0.015 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 17 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.291 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1416 time to fit residues: 3.2196 Evaluate side-chains 17 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2537 Z= 0.121 Angle : 0.371 5.754 3499 Z= 0.227 Chirality : 0.038 0.116 442 Planarity : 0.003 0.055 482 Dihedral : 3.488 16.683 449 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: 2.86 (0.43), residues: 434 helix: 2.90 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.91 (0.64), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B2296 HIS 0.008 0.001 HIS A 38 PHE 0.015 0.001 PHE B2295 TYR 0.007 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 20 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.297 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1371 time to fit residues: 3.4776 Evaluate side-chains 18 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.4187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092588 restraints weight = 8245.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093984 restraints weight = 5379.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094834 restraints weight = 3951.036| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2537 Z= 0.166 Angle : 0.388 4.577 3499 Z= 0.238 Chirality : 0.038 0.104 442 Planarity : 0.004 0.064 482 Dihedral : 3.826 15.465 449 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.61 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 17.91 % 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: 2.52 (0.43), residues: 434 helix: 2.59 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.11 (0.66), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.006 0.001 HIS A 38 PHE 0.015 0.002 PHE B2295 TYR 0.009 0.001 TYR B2310 ARG 0.002 0.000 ARG B2387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 799.61 seconds wall clock time: 15 minutes 13.05 seconds (913.05 seconds total)