Starting phenix.real_space_refine on Sun Mar 10 21:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/03_2024/8d8q_27254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/03_2024/8d8q_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_27254/03_2024/8d8q_27254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/03_2024/8d8q_27254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/03_2024/8d8q_27254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8q_27254/03_2024/8d8q_27254.pdb" } resolution = 4.2 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= 0.044 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 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. 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-5265/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.44, per 1000 atoms: 0.66 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: 1.91 Conformation dependent library (CDL) restraints added in 966.8 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: 0.74 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: 1.58 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: 3013 16.62 - 33.25: 85 33.25 - 49.87: 24 49.87 - 66.49: 18 66.49 - 83.11: 8 Dihedral angle restraints: 3148 sinusoidal: 1232 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 3145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 421 0.037 - 0.075: 238 0.075 - 0.112: 88 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 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: 5.500 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: 28.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.012 0.066 5327 Z= 0.732 Angle : 1.230 7.760 7228 Z= 0.851 Chirality : 0.054 0.187 780 Planarity : 0.005 0.027 927 Dihedral : 11.021 83.112 1917 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 % Allowed : 1.06 % Favored : 98.40 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 436 HIS 0.003 0.001 HIS B 90 PHE 0.015 0.004 PHE H 67 TYR 0.030 0.005 TYR A 489 ARG 0.002 0.000 ARG H 66 *********************** 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 : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.6548 (m-80) cc_final: 0.5847 (m-80) REVERT: H 120 LEU cc_start: 0.8426 (tp) cc_final: 0.7602 (pp) REVERT: L 3 VAL cc_start: 0.8346 (t) cc_final: 0.8091 (m) REVERT: L 46 LEU cc_start: 0.8987 (tp) cc_final: 0.8671 (tp) REVERT: L 72 THR cc_start: 0.7216 (m) cc_final: 0.6987 (m) REVERT: L 78 LEU cc_start: 0.8328 (tp) cc_final: 0.7927 (tp) REVERT: L 85 ILE cc_start: 0.8790 (mm) cc_final: 0.8154 (tp) REVERT: A 355 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7329 (ttp-170) REVERT: A 461 LEU cc_start: 0.8715 (mt) cc_final: 0.8506 (mp) REVERT: B 14 SER cc_start: 0.8112 (m) cc_final: 0.7637 (t) REVERT: B 36 TYR cc_start: 0.7400 (m-80) cc_final: 0.6903 (m-80) REVERT: B 46 LEU cc_start: 0.8577 (tp) cc_final: 0.8179 (tp) REVERT: B 47 LEU cc_start: 0.7761 (mp) cc_final: 0.7494 (mt) REVERT: C 18 VAL cc_start: 0.8846 (p) cc_final: 0.8563 (p) REVERT: C 36 TRP cc_start: 0.8957 (m100) cc_final: 0.8585 (m100) REVERT: C 46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7843 (tp30) REVERT: C 51 ILE cc_start: 0.8990 (tt) cc_final: 0.8760 (tt) REVERT: C 70 THR cc_start: 0.8531 (p) cc_final: 0.8182 (t) REVERT: C 72 ASP cc_start: 0.8597 (t0) cc_final: 0.7883 (t70) outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.2276 time to fit residues: 64.1006 Evaluate side-chains 121 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 0.0050 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8114 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5327 Z= 0.189 Angle : 0.623 9.968 7228 Z= 0.339 Chirality : 0.047 0.301 780 Planarity : 0.005 0.039 927 Dihedral : 4.842 18.194 759 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.57 % Rotamer: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.52 % 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: 1.28 (0.33), residues: 659 helix: -3.75 (0.56), residues: 33 sheet: 0.69 (0.32), residues: 237 loop : 1.63 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 115 HIS 0.001 0.001 HIS B 90 PHE 0.018 0.002 PHE C 29 TYR 0.020 0.001 TYR L 49 ARG 0.006 0.001 ARG A 403 *********************** 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 178 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8096 (mmm) cc_final: 0.7872 (mmm) REVERT: H 39 GLN cc_start: 0.7673 (pp30) cc_final: 0.7323 (pp30) REVERT: H 111 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7616 (mttt) REVERT: H 113 ASP cc_start: 0.7334 (t70) cc_final: 0.6538 (p0) REVERT: H 120 LEU cc_start: 0.8483 (tp) cc_final: 0.7699 (pp) REVERT: L 3 VAL cc_start: 0.8226 (t) cc_final: 0.8006 (m) REVERT: L 58 VAL cc_start: 0.8499 (t) cc_final: 0.8268 (p) REVERT: L 103 LYS cc_start: 0.8621 (tttt) cc_final: 0.8162 (tptm) REVERT: A 355 ARG cc_start: 0.7525 (ttt90) cc_final: 0.7219 (ttp-170) REVERT: A 398 ASP cc_start: 0.8430 (m-30) cc_final: 0.8166 (m-30) REVERT: A 402 ILE cc_start: 0.8774 (pt) cc_final: 0.8543 (pt) REVERT: C 4 LEU cc_start: 0.8093 (mt) cc_final: 0.7611 (mt) REVERT: C 18 VAL cc_start: 0.8676 (p) cc_final: 0.8119 (p) REVERT: C 36 TRP cc_start: 0.8864 (m100) cc_final: 0.8555 (m100) REVERT: C 46 GLU cc_start: 0.8258 (tt0) cc_final: 0.7962 (tp30) REVERT: C 70 THR cc_start: 0.8547 (p) cc_final: 0.8259 (t) REVERT: C 71 ARG cc_start: 0.7705 (pmt-80) cc_final: 0.7158 (pmt-80) REVERT: C 72 ASP cc_start: 0.8556 (t0) cc_final: 0.7884 (t70) REVERT: C 73 MET cc_start: 0.7312 (pmm) cc_final: 0.6817 (pmm) REVERT: C 82 LEU cc_start: 0.7953 (tp) cc_final: 0.7675 (tp) REVERT: C 86 ASP cc_start: 0.7924 (m-30) cc_final: 0.7700 (m-30) REVERT: C 91 TYR cc_start: 0.9082 (m-80) cc_final: 0.8872 (m-10) REVERT: C 104 ASP cc_start: 0.8551 (m-30) cc_final: 0.8229 (m-30) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1963 time to fit residues: 43.8044 Evaluate side-chains 119 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5327 Z= 0.250 Angle : 0.621 9.515 7228 Z= 0.339 Chirality : 0.046 0.249 780 Planarity : 0.005 0.042 927 Dihedral : 4.748 16.179 759 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.19 % Favored : 96.66 % Rotamer: Outliers : 0.18 % Allowed : 1.77 % Favored : 98.05 % 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: 0.73 (0.33), residues: 659 helix: -3.46 (0.65), residues: 33 sheet: 0.50 (0.32), residues: 240 loop : 1.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 96 HIS 0.002 0.001 HIS B 90 PHE 0.024 0.002 PHE H 67 TYR 0.032 0.002 TYR H 99 ARG 0.005 0.001 ARG A 357 *********************** 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 155 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8237 (mmm) cc_final: 0.7915 (mmm) REVERT: H 39 GLN cc_start: 0.7935 (pp30) cc_final: 0.7317 (pp30) REVERT: H 67 PHE cc_start: 0.5989 (m-80) cc_final: 0.5615 (m-80) REVERT: H 113 ASP cc_start: 0.7246 (t70) cc_final: 0.6987 (p0) REVERT: L 3 VAL cc_start: 0.8125 (t) cc_final: 0.7913 (m) REVERT: L 30 LEU cc_start: 0.8450 (tp) cc_final: 0.8027 (tp) REVERT: L 30 TYR cc_start: 0.8217 (t80) cc_final: 0.7698 (t80) REVERT: L 103 LYS cc_start: 0.8727 (tttt) cc_final: 0.8495 (ttpt) REVERT: A 355 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7391 (ttp-170) REVERT: A 357 ARG cc_start: 0.8349 (ttm110) cc_final: 0.8141 (ttm110) REVERT: A 402 ILE cc_start: 0.8861 (pt) cc_final: 0.8656 (pt) REVERT: C 36 TRP cc_start: 0.9170 (m100) cc_final: 0.8776 (m100) REVERT: C 71 ARG cc_start: 0.7721 (pmt-80) cc_final: 0.7167 (pmt-80) REVERT: C 72 ASP cc_start: 0.8648 (t0) cc_final: 0.7746 (t70) REVERT: C 73 MET cc_start: 0.7508 (pmm) cc_final: 0.6872 (pmm) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1856 time to fit residues: 36.5865 Evaluate side-chains 104 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 0.8980 chunk 44 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- 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** B 90 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5327 Z= 0.213 Angle : 0.574 7.643 7228 Z= 0.317 Chirality : 0.046 0.292 780 Planarity : 0.004 0.040 927 Dihedral : 4.577 17.452 759 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.36 % Rotamer: Outliers : 0.18 % Allowed : 1.77 % Favored : 98.05 % 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: 0.48 (0.33), residues: 659 helix: -3.45 (0.68), residues: 33 sheet: 0.41 (0.33), residues: 240 loop : 0.80 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 96 HIS 0.002 0.001 HIS B 90 PHE 0.018 0.002 PHE A 374 TYR 0.024 0.002 TYR H 99 ARG 0.006 0.001 ARG B 18 *********************** 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 145 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7932 (pp30) cc_final: 0.7250 (pp30) REVERT: L 3 VAL cc_start: 0.8169 (t) cc_final: 0.7952 (m) REVERT: L 30 TYR cc_start: 0.8318 (t80) cc_final: 0.7981 (t80) REVERT: L 48 MET cc_start: 0.7311 (tpp) cc_final: 0.6537 (mmm) REVERT: L 103 LYS cc_start: 0.8654 (tttt) cc_final: 0.8185 (tptm) REVERT: A 340 GLU cc_start: 0.8769 (mp0) cc_final: 0.8414 (tp30) REVERT: A 355 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7232 (ttp-170) REVERT: A 402 ILE cc_start: 0.8775 (pt) cc_final: 0.8523 (pt) REVERT: A 455 LEU cc_start: 0.8464 (tp) cc_final: 0.8226 (tp) REVERT: C 36 TRP cc_start: 0.9234 (m100) cc_final: 0.8856 (m100) REVERT: C 70 THR cc_start: 0.8449 (p) cc_final: 0.7932 (t) REVERT: C 71 ARG cc_start: 0.7717 (pmt-80) cc_final: 0.7202 (pmt-80) REVERT: C 72 ASP cc_start: 0.8698 (t0) cc_final: 0.7682 (t70) REVERT: C 73 MET cc_start: 0.7524 (pmm) cc_final: 0.7096 (pmm) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1799 time to fit residues: 33.4195 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 GLN 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** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.006 0.061 5327 Z= 0.419 Angle : 0.738 11.820 7228 Z= 0.399 Chirality : 0.050 0.381 780 Planarity : 0.005 0.043 927 Dihedral : 5.433 17.683 759 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -0.12 (0.33), residues: 659 helix: -3.72 (0.61), residues: 33 sheet: 0.21 (0.33), residues: 250 loop : 0.19 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 96 HIS 0.004 0.002 HIS B 90 PHE 0.021 0.003 PHE A 374 TYR 0.034 0.003 TYR H 99 ARG 0.009 0.001 ARG H 30 *********************** 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 139 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8202 (mmm) cc_final: 0.7953 (mmm) REVERT: L 30 TYR cc_start: 0.8628 (t80) cc_final: 0.8372 (t80) REVERT: A 340 GLU cc_start: 0.8836 (mp0) cc_final: 0.8320 (tp30) REVERT: A 355 ARG cc_start: 0.7709 (ttt90) cc_final: 0.7196 (ttp-170) REVERT: A 455 LEU cc_start: 0.8592 (tp) cc_final: 0.8327 (tp) REVERT: B 46 LEU cc_start: 0.8563 (tp) cc_final: 0.8289 (tp) REVERT: C 61 GLN cc_start: 0.9094 (mt0) cc_final: 0.8394 (mp10) REVERT: C 72 ASP cc_start: 0.8780 (t0) cc_final: 0.7619 (t70) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1734 time to fit residues: 31.5213 Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** L 89 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5327 Z= 0.198 Angle : 0.638 11.132 7228 Z= 0.344 Chirality : 0.047 0.285 780 Planarity : 0.004 0.048 927 Dihedral : 4.973 20.202 759 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 (0.32), residues: 659 helix: -4.01 (0.60), residues: 33 sheet: 0.24 (0.33), residues: 244 loop : 0.08 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.002 0.001 HIS B 90 PHE 0.016 0.002 PHE B 71 TYR 0.013 0.002 TYR H 91 ARG 0.008 0.001 ARG B 24 *********************** 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 135 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8310 (mmm) cc_final: 0.8031 (mmm) REVERT: L 30 TYR cc_start: 0.8584 (t80) cc_final: 0.8057 (t80) REVERT: L 49 TYR cc_start: 0.6992 (p90) cc_final: 0.6229 (p90) REVERT: A 340 GLU cc_start: 0.8818 (mp0) cc_final: 0.8339 (tp30) REVERT: A 455 LEU cc_start: 0.8590 (tp) cc_final: 0.8344 (tp) REVERT: B 46 LEU cc_start: 0.8446 (tp) cc_final: 0.8154 (tp) REVERT: C 61 GLN cc_start: 0.9069 (mt0) cc_final: 0.8352 (mp10) REVERT: C 72 ASP cc_start: 0.8603 (t0) cc_final: 0.7543 (t70) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1828 time to fit residues: 31.8258 Evaluate side-chains 101 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6019 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= 0.211 Angle : 0.607 8.972 7228 Z= 0.334 Chirality : 0.045 0.208 780 Planarity : 0.004 0.053 927 Dihedral : 4.983 21.354 759 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.37 (0.32), residues: 659 helix: -4.16 (0.59), residues: 33 sheet: 0.01 (0.32), residues: 254 loop : 0.09 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 353 HIS 0.002 0.001 HIS B 90 PHE 0.030 0.002 PHE C 29 TYR 0.021 0.002 TYR C 59 ARG 0.005 0.000 ARG A 357 *********************** 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 130 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8397 (mmm) cc_final: 0.8143 (mmm) REVERT: L 30 TYR cc_start: 0.8680 (t80) cc_final: 0.8229 (t80) REVERT: L 103 LYS cc_start: 0.8638 (tttt) cc_final: 0.8104 (tptt) REVERT: A 340 GLU cc_start: 0.8826 (mp0) cc_final: 0.8379 (tp30) REVERT: A 455 LEU cc_start: 0.8634 (tp) cc_final: 0.8392 (tp) REVERT: C 61 GLN cc_start: 0.9070 (mt0) cc_final: 0.8407 (mp10) REVERT: C 72 ASP cc_start: 0.8758 (t0) cc_final: 0.7733 (t70) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1788 time to fit residues: 30.0477 Evaluate side-chains 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 7.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6168 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= 0.170 Angle : 0.589 8.110 7228 Z= 0.319 Chirality : 0.045 0.173 780 Planarity : 0.004 0.050 927 Dihedral : 4.747 21.672 759 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.39 (0.32), residues: 659 helix: -4.19 (0.58), residues: 33 sheet: 0.07 (0.33), residues: 242 loop : 0.01 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.001 0.001 HIS B 90 PHE 0.022 0.002 PHE C 29 TYR 0.017 0.001 TYR H 99 ARG 0.006 0.001 ARG A 357 *********************** 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 133 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8344 (mmm) cc_final: 0.8108 (mmm) REVERT: L 30 TYR cc_start: 0.8613 (t80) cc_final: 0.8113 (t80) REVERT: L 85 ILE cc_start: 0.8638 (mm) cc_final: 0.7893 (tt) REVERT: L 103 LYS cc_start: 0.8630 (tttt) cc_final: 0.8150 (tptt) REVERT: A 340 GLU cc_start: 0.8743 (mp0) cc_final: 0.8284 (tp30) REVERT: A 455 LEU cc_start: 0.8590 (tp) cc_final: 0.8366 (tp) REVERT: B 46 LEU cc_start: 0.8345 (tp) cc_final: 0.8114 (tp) REVERT: B 105 GLU cc_start: 0.4962 (tp30) cc_final: 0.4570 (tp30) REVERT: C 36 TRP cc_start: 0.9331 (m100) cc_final: 0.8960 (m100) REVERT: C 51 ILE cc_start: 0.8936 (tt) cc_final: 0.8694 (tt) REVERT: C 61 GLN cc_start: 0.9081 (mt0) cc_final: 0.8366 (mp10) REVERT: C 72 ASP cc_start: 0.8680 (t0) cc_final: 0.7641 (t70) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1859 time to fit residues: 31.4363 Evaluate side-chains 102 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 38 GLN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5327 Z= 0.271 Angle : 0.636 6.626 7228 Z= 0.345 Chirality : 0.047 0.177 780 Planarity : 0.005 0.049 927 Dihedral : 4.980 21.517 759 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.18 % Allowed : 0.71 % Favored : 99.11 % 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: -0.66 (0.32), residues: 659 helix: -4.09 (0.57), residues: 33 sheet: -0.01 (0.33), residues: 241 loop : -0.29 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 96 HIS 0.001 0.001 HIS A 519 PHE 0.025 0.002 PHE C 29 TYR 0.020 0.002 TYR H 99 ARG 0.006 0.001 ARG H 19 *********************** 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 : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8400 (mmm) cc_final: 0.8109 (mmm) REVERT: L 30 TYR cc_start: 0.8757 (t80) cc_final: 0.8456 (t80) REVERT: L 103 LYS cc_start: 0.8623 (tttt) cc_final: 0.8109 (tptt) REVERT: A 340 GLU cc_start: 0.8782 (mp0) cc_final: 0.8279 (tp30) REVERT: A 455 LEU cc_start: 0.8695 (tp) cc_final: 0.8454 (tp) REVERT: B 87 TYR cc_start: 0.8059 (m-80) cc_final: 0.7689 (m-10) REVERT: C 10 GLU cc_start: 0.8001 (pp20) cc_final: 0.7619 (pp20) REVERT: C 30 MET cc_start: 0.6898 (tpt) cc_final: 0.6671 (tpt) REVERT: C 61 GLN cc_start: 0.9107 (mt0) cc_final: 0.8419 (mp10) REVERT: C 72 ASP cc_start: 0.8623 (t0) cc_final: 0.7728 (t70) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1696 time to fit residues: 27.8751 Evaluate side-chains 93 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 0.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30EASN A 481 ASN B 38 GLN C 39 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5327 Z= 0.167 Angle : 0.584 6.209 7228 Z= 0.318 Chirality : 0.047 0.299 780 Planarity : 0.004 0.047 927 Dihedral : 4.750 20.983 759 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.18 % Allowed : 0.71 % Favored : 99.11 % 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 (0.32), residues: 659 helix: -4.16 (0.60), residues: 33 sheet: -0.05 (0.33), residues: 241 loop : -0.18 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.000 0.000 HIS B 90 PHE 0.025 0.002 PHE C 29 TYR 0.039 0.002 TYR B 87 ARG 0.007 0.001 ARG A 357 ********************** 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 137 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8369 (mmm) cc_final: 0.8134 (mmm) REVERT: H 43 LYS cc_start: 0.8686 (mppt) cc_final: 0.8425 (mmtt) REVERT: H 81 GLN cc_start: 0.7326 (tp40) cc_final: 0.6469 (tm-30) REVERT: H 120 LEU cc_start: 0.8737 (mm) cc_final: 0.8306 (pp) REVERT: L 30 TYR cc_start: 0.8639 (t80) cc_final: 0.8256 (t80) REVERT: L 85 ILE cc_start: 0.8593 (mm) cc_final: 0.7987 (tp) REVERT: L 103 LYS cc_start: 0.8602 (tttt) cc_final: 0.8135 (tptt) REVERT: A 340 GLU cc_start: 0.8725 (mp0) cc_final: 0.8261 (tp30) REVERT: A 422 ASN cc_start: 0.8824 (m-40) cc_final: 0.8078 (m-40) REVERT: A 455 LEU cc_start: 0.8655 (tp) cc_final: 0.8420 (tp) REVERT: B 71 PHE cc_start: 0.7373 (m-10) cc_final: 0.7155 (m-10) REVERT: C 36 TRP cc_start: 0.9296 (m100) cc_final: 0.9051 (m100) REVERT: C 61 GLN cc_start: 0.9075 (mt0) cc_final: 0.8383 (mp10) REVERT: C 72 ASP cc_start: 0.8489 (t0) cc_final: 0.7761 (t70) REVERT: C 77 THR cc_start: 0.8691 (m) cc_final: 0.8445 (m) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1769 time to fit residues: 30.7829 Evaluate side-chains 106 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 30.0000 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077701 restraints weight = 18422.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079934 restraints weight = 10717.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.081412 restraints weight = 7335.850| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5327 Z= 0.167 Angle : 0.590 7.202 7228 Z= 0.317 Chirality : 0.045 0.171 780 Planarity : 0.004 0.044 927 Dihedral : 4.643 21.476 759 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.62 (0.33), residues: 659 helix: -4.14 (0.58), residues: 33 sheet: -0.07 (0.33), residues: 241 loop : -0.19 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 50 HIS 0.001 0.000 HIS B 90 PHE 0.028 0.002 PHE C 29 TYR 0.016 0.001 TYR L 49 ARG 0.006 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1855.98 seconds wall clock time: 34 minutes 15.62 seconds (2055.62 seconds total)