Starting phenix.real_space_refine (version: dev) on Fri Feb 17 14:56:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/02_2023/8d8q_27254.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.044 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 Process input model Symmetric amino acids flipped Residue "A GLU 484": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5202 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 996 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "L" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.70, per 1000 atoms: 0.71 Number of scatterers: 5202 At special positions: 0 Unit cell: (77.996, 94.86, 102.238, 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 27 16.00 O 1010 8.00 N 874 7.00 C 3291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.12 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.12 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 102 " distance=2.05 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 790.8 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 11.4% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 30B through 30F removed outlier: 4.153A pdb=" N LYS L 30F" --> pdb=" O SER L 30C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.089A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 30 through 31 No H-bonds generated for 'chain 'B' and resid 30 through 31' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.540A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.826A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.707A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.587A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.544A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.551A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.551A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 97 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.116A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 205 hydrogen bonds defined for protein. 456 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: 1.71 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1000 1.32 - 1.45: 1457 1.45 - 1.57: 2834 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 5327 Sorted by residual: bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.449 0.063 2.20e-02 2.07e+03 8.16e+00 bond pdb=" CG ASP H 58 " pdb=" OD1 ASP H 58 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.25e+00 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 1.530 1.479 0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CD GLU H 6 " pdb=" OE2 GLU H 6 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.40e+00 ... (remaining 5322 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 127 105.94 - 112.97: 2679 112.97 - 119.99: 1842 119.99 - 127.02: 2534 127.02 - 134.05: 46 Bond angle restraints: 7228 Sorted by residual: angle pdb=" C GLN L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" C GLY H 104 " pdb=" N PRO H 105 " pdb=" CA PRO H 105 " ideal model delta sigma weight residual 119.56 126.58 -7.02 1.01e+00 9.80e-01 4.83e+01 angle pdb=" C ILE B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 119.78 126.73 -6.95 1.03e+00 9.43e-01 4.55e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.47 127.11 -7.64 1.16e+00 7.43e-01 4.34e+01 ... (remaining 7223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 2998 16.62 - 33.25: 85 33.25 - 49.87: 24 49.87 - 66.49: 18 66.49 - 83.11: 8 Dihedral angle restraints: 3133 sinusoidal: 1217 harmonic: 1916 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.82 -52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.71 36.29 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.01 -32.01 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 423 0.037 - 0.075: 237 0.075 - 0.112: 87 0.112 - 0.150: 24 0.150 - 0.187: 9 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 777 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.34e+00 pdb=" CG TYR A 489 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " 0.027 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR L 32 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 449 " -0.025 2.00e-02 2.50e+03 1.37e-02 3.74e+00 pdb=" CG TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 449 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 449 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 449 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 449 " -0.021 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 157 2.69 - 3.24: 4892 3.24 - 3.80: 8245 3.80 - 4.35: 11033 4.35 - 4.90: 18057 Nonbonded interactions: 42384 Sorted by model distance: nonbonded pdb=" N TYR L 49 " pdb=" CD1 TYR L 49 " model vdw 2.139 3.420 nonbonded pdb=" O LYS H 111 " pdb=" OH TYR H 114 " model vdw 2.458 2.440 nonbonded pdb=" O TYR L 30A" pdb=" N SER L 30C" model vdw 2.487 2.520 nonbonded pdb=" O SER L 93 " pdb=" OG1 THR L 94 " model vdw 2.490 2.440 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.498 2.520 ... (remaining 42379 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3291 2.51 5 N 874 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 7.970 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: 29.230 Check model and map are aligned: 0.080 Process input model: 18.700 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.011 0.066 5327 Z= 0.730 Angle : 1.228 7.760 7228 Z= 0.851 Chirality : 0.054 0.187 780 Planarity : 0.005 0.027 927 Dihedral : 11.061 83.112 1902 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.52 % Favored : 98.33 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.35), residues: 659 helix: -4.41 (0.31), residues: 33 sheet: 1.24 (0.31), residues: 256 loop : 2.53 (0.36), residues: 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.2296 time to fit residues: 64.8509 Evaluate side-chains 114 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.708 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0816 time to fit residues: 1.2105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 30EASN L 37 GLN B 6 GLN C 1 GLN C 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 5327 Z= 0.181 Angle : 0.631 9.171 7228 Z= 0.342 Chirality : 0.048 0.283 780 Planarity : 0.005 0.042 927 Dihedral : 4.886 18.063 744 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.57 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.33), residues: 659 helix: -3.77 (0.56), residues: 33 sheet: 0.74 (0.32), residues: 234 loop : 1.63 (0.33), residues: 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1838 time to fit residues: 40.3107 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 0.0000 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN B 89 GLN C 35 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 5327 Z= 0.189 Angle : 0.587 7.983 7228 Z= 0.319 Chirality : 0.046 0.250 780 Planarity : 0.004 0.042 927 Dihedral : 4.653 18.712 744 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.88 % Favored : 96.97 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.80 (0.33), residues: 659 helix: -3.56 (0.63), residues: 33 sheet: 0.56 (0.32), residues: 237 loop : 1.10 (0.33), residues: 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1885 time to fit residues: 36.6411 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 5327 Z= 0.212 Angle : 0.588 7.583 7228 Z= 0.320 Chirality : 0.046 0.302 780 Planarity : 0.004 0.040 927 Dihedral : 4.563 16.927 744 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.60 (0.33), residues: 659 helix: -3.41 (0.68), residues: 33 sheet: 0.47 (0.31), residues: 250 loop : 0.91 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1760 time to fit residues: 35.1314 Evaluate side-chains 99 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 GLN ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN B 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 5327 Z= 0.343 Angle : 0.699 12.807 7228 Z= 0.378 Chirality : 0.049 0.354 780 Planarity : 0.005 0.045 927 Dihedral : 5.237 19.500 744 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.23 (0.33), residues: 659 helix: -3.72 (0.63), residues: 33 sheet: 0.51 (0.33), residues: 239 loop : 0.41 (0.33), residues: 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1697 time to fit residues: 30.2594 Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 89 GLN ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5327 Z= 0.182 Angle : 0.597 11.203 7228 Z= 0.323 Chirality : 0.045 0.249 780 Planarity : 0.004 0.046 927 Dihedral : 4.799 19.698 744 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.18 (0.33), residues: 659 helix: -3.91 (0.56), residues: 33 sheet: 0.54 (0.34), residues: 240 loop : 0.34 (0.32), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1814 time to fit residues: 32.0061 Evaluate side-chains 92 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.0370 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 overall best weight: 2.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN B 90 HIS ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5327 Z= 0.240 Angle : 0.627 8.126 7228 Z= 0.339 Chirality : 0.046 0.225 780 Planarity : 0.004 0.046 927 Dihedral : 4.985 19.947 744 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.01 (0.33), residues: 659 helix: -3.96 (0.65), residues: 27 sheet: 0.40 (0.33), residues: 245 loop : 0.13 (0.32), residues: 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1746 time to fit residues: 31.1215 Evaluate side-chains 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5327 Z= 0.186 Angle : 0.578 6.871 7228 Z= 0.313 Chirality : 0.044 0.156 780 Planarity : 0.004 0.045 927 Dihedral : 4.689 19.625 744 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.01 (0.33), residues: 659 helix: -4.03 (0.65), residues: 27 sheet: 0.47 (0.33), residues: 244 loop : 0.11 (0.32), residues: 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1815 time to fit residues: 32.1299 Evaluate side-chains 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN B 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5327 Z= 0.208 Angle : 0.605 6.768 7228 Z= 0.330 Chirality : 0.044 0.156 780 Planarity : 0.004 0.044 927 Dihedral : 4.887 24.771 744 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.24 (0.33), residues: 659 helix: -4.13 (0.62), residues: 27 sheet: 0.39 (0.34), residues: 236 loop : -0.14 (0.31), residues: 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1654 time to fit residues: 27.5737 Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5327 Z= 0.168 Angle : 0.602 9.925 7228 Z= 0.323 Chirality : 0.045 0.152 780 Planarity : 0.004 0.045 927 Dihedral : 4.741 23.846 744 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.19 (0.33), residues: 659 helix: -4.05 (0.66), residues: 27 sheet: 0.51 (0.35), residues: 236 loop : -0.16 (0.32), residues: 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1912 time to fit residues: 33.6266 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 30EASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079009 restraints weight = 17980.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081240 restraints weight = 10395.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082705 restraints weight = 7086.239| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5327 Z= 0.167 Angle : 0.591 9.410 7228 Z= 0.316 Chirality : 0.044 0.154 780 Planarity : 0.004 0.045 927 Dihedral : 4.645 23.571 744 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.21 (0.33), residues: 659 helix: -4.02 (0.66), residues: 27 sheet: 0.48 (0.35), residues: 238 loop : -0.18 (0.32), residues: 394 =============================================================================== Job complete usr+sys time: 1881.48 seconds wall clock time: 35 minutes 26.16 seconds (2126.16 seconds total)