Starting phenix.real_space_refine on Mon Sep 23 20:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey5_31378/09_2024/7ey5_31378_neut.cif" } resolution = 3.4 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= -0.001 sd= 0.039 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 20 5.16 5 C 3237 2.51 5 N 845 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5072 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 4.63, per 1000 atoms: 0.91 Number of scatterers: 5072 At special positions: 0 Unit cell: (95.92, 92.65, 109, 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 20 16.00 O 970 8.00 N 845 7.00 C 3237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 603.5 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 7.3% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.624A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.854A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.733A 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 438 through 443 removed outlier: 3.528A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.908A pdb=" N ALA H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.503A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.449A pdb=" N GLU B 16 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.951A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 115 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.598A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.872A pdb=" N LEU C 11 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 106 " --> pdb=" O LEU C 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.677A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.217A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 103 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.564A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR L 69 " --> pdb=" O THR L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 303 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: 1.22 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1598 1.34 - 1.46: 1411 1.46 - 1.58: 2175 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 5209 Sorted by residual: bond pdb=" CD2 TYR L 91 " pdb=" CE2 TYR L 91 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB MET B 48 " pdb=" CG MET B 48 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB VAL H 48 " pdb=" CG1 VAL H 48 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.20e-02 2.07e+03 9.47e-01 bond pdb=" CA ASN B 105 " pdb=" CB ASN B 105 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.54e-02 4.22e+03 8.81e-01 ... (remaining 5204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 6948 2.50 - 5.00: 113 5.00 - 7.49: 10 7.49 - 9.99: 1 9.99 - 12.49: 3 Bond angle restraints: 7075 Sorted by residual: angle pdb=" N GLY B 113 " pdb=" CA GLY B 113 " pdb=" C GLY B 113 " ideal model delta sigma weight residual 113.18 102.33 10.85 2.37e+00 1.78e-01 2.09e+01 angle pdb=" CA LEU B 115 " pdb=" CB LEU B 115 " pdb=" CG LEU B 115 " ideal model delta sigma weight residual 116.30 103.81 12.49 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C VAL C 13 " pdb=" N SER C 14 " pdb=" CA SER C 14 " ideal model delta sigma weight residual 120.97 130.81 -9.84 2.84e+00 1.24e-01 1.20e+01 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 119.58 -5.68 1.80e+00 3.09e-01 9.95e+00 angle pdb=" C VAL H 12 " pdb=" N LYS H 13 " pdb=" CA LYS H 13 " ideal model delta sigma weight residual 121.95 133.22 -11.27 3.74e+00 7.15e-02 9.08e+00 ... (remaining 7070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2701 16.91 - 33.81: 283 33.81 - 50.72: 38 50.72 - 67.63: 12 67.63 - 84.53: 6 Dihedral angle restraints: 3040 sinusoidal: 1181 harmonic: 1859 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -153.03 67.03 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CA THR B 114 " pdb=" C THR B 114 " pdb=" N LEU B 115 " pdb=" CA LEU B 115 " ideal model delta harmonic sigma weight residual -180.00 -147.39 -32.61 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN B 31 " pdb=" C ASN B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta harmonic sigma weight residual -180.00 -148.73 -31.27 0 5.00e+00 4.00e-02 3.91e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 628 0.066 - 0.131: 111 0.131 - 0.197: 6 0.197 - 0.263: 1 0.263 - 0.329: 1 Chirality restraints: 747 Sorted by residual: chirality pdb=" CG LEU B 115 " pdb=" CB LEU B 115 " pdb=" CD1 LEU B 115 " pdb=" CD2 LEU B 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 744 not shown) Planarity restraints: 906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 110 " -0.019 2.00e-02 2.50e+03 1.76e-02 7.74e+00 pdb=" CG TRP B 110 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 110 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 110 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 110 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 110 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 106 " -0.028 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP B 106 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 106 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 106 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 106 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 106 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 106 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 106 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 106 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 106 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 29 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 30 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.033 5.00e-02 4.00e+02 ... (remaining 903 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 241 2.71 - 3.26: 5068 3.26 - 3.80: 7726 3.80 - 4.35: 9597 4.35 - 4.90: 16730 Nonbonded interactions: 39362 Sorted by model distance: nonbonded pdb=" NE2 GLN L 6 " pdb=" O TYR L 86 " model vdw 2.161 3.120 nonbonded pdb=" OG SER C 26 " pdb=" OE1 GLN C 27 " model vdw 2.194 3.040 nonbonded pdb=" NH1 ARG H 38 " pdb=" OE2 GLU H 46 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.200 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.208 3.040 ... (remaining 39357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 8.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.005 0.037 5209 Z= 0.331 Angle : 0.807 12.490 7075 Z= 0.431 Chirality : 0.050 0.329 747 Planarity : 0.005 0.060 906 Dihedral : 13.838 84.534 1845 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.63 (0.29), residues: 638 helix: -4.24 (0.41), residues: 32 sheet: -1.61 (0.35), residues: 227 loop : -2.87 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 110 HIS 0.002 0.001 HIS B 82 PHE 0.019 0.001 PHE H 11 TYR 0.037 0.002 TYR L 91 ARG 0.012 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8657 (p0) cc_final: 0.8263 (p0) REVERT: C 18 ARG cc_start: 0.7110 (ttp80) cc_final: 0.6855 (ttp80) REVERT: C 42 GLN cc_start: 0.7144 (pp30) cc_final: 0.6942 (pp30) REVERT: H 116 TYR cc_start: 0.8166 (p90) cc_final: 0.7934 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2541 time to fit residues: 35.6588 Evaluate side-chains 96 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5209 Z= 0.178 Angle : 0.692 8.954 7075 Z= 0.368 Chirality : 0.047 0.144 747 Planarity : 0.005 0.050 906 Dihedral : 6.086 29.012 712 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.36 % Allowed : 9.82 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -3.05 (0.30), residues: 638 helix: -3.85 (0.50), residues: 32 sheet: -0.80 (0.36), residues: 222 loop : -2.76 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 106 HIS 0.001 0.001 HIS B 82 PHE 0.010 0.001 PHE B 64 TYR 0.021 0.001 TYR L 91 ARG 0.004 0.000 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8676 (p0) cc_final: 0.8253 (p0) REVERT: B 3 GLN cc_start: 0.8035 (pp30) cc_final: 0.7500 (pp30) REVERT: C 18 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6739 (ttp80) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2285 time to fit residues: 34.6098 Evaluate side-chains 109 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5209 Z= 0.325 Angle : 0.741 9.389 7075 Z= 0.390 Chirality : 0.047 0.191 747 Planarity : 0.005 0.047 906 Dihedral : 6.270 32.140 712 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 1.64 % Allowed : 13.45 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.08 (0.30), residues: 638 helix: -3.70 (0.56), residues: 32 sheet: -0.86 (0.36), residues: 223 loop : -2.78 (0.26), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 106 HIS 0.001 0.001 HIS B 82 PHE 0.016 0.001 PHE L 71 TYR 0.016 0.002 TYR C 91 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8671 (p0) cc_final: 0.8227 (p0) REVERT: A 442 ASP cc_start: 0.8182 (m-30) cc_final: 0.7964 (m-30) REVERT: B 3 GLN cc_start: 0.8105 (pp30) cc_final: 0.7681 (pp30) REVERT: C 18 ARG cc_start: 0.7014 (ttp80) cc_final: 0.6710 (ttp80) REVERT: H 116 TYR cc_start: 0.8757 (p90) cc_final: 0.8440 (p90) outliers start: 9 outliers final: 5 residues processed: 114 average time/residue: 0.2247 time to fit residues: 31.3483 Evaluate side-chains 106 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5209 Z= 0.273 Angle : 0.728 9.526 7075 Z= 0.382 Chirality : 0.046 0.154 747 Planarity : 0.005 0.047 906 Dihedral : 6.078 29.532 712 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.55 % Allowed : 16.18 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.87 (0.30), residues: 638 helix: -3.64 (0.70), residues: 26 sheet: -0.78 (0.36), residues: 223 loop : -2.60 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 106 HIS 0.002 0.001 HIS B 82 PHE 0.013 0.001 PHE L 71 TYR 0.017 0.001 TYR L 91 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8692 (p0) cc_final: 0.8269 (p0) REVERT: A 442 ASP cc_start: 0.8120 (m-30) cc_final: 0.7876 (m-30) REVERT: B 3 GLN cc_start: 0.8128 (pp30) cc_final: 0.7741 (pp30) REVERT: C 18 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6696 (ttp80) REVERT: H 78 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8555 (ptpp) outliers start: 14 outliers final: 10 residues processed: 114 average time/residue: 0.2438 time to fit residues: 34.5233 Evaluate side-chains 112 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 0.0030 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5209 Z= 0.195 Angle : 0.701 10.707 7075 Z= 0.364 Chirality : 0.045 0.196 747 Planarity : 0.005 0.047 906 Dihedral : 5.766 27.493 712 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.64 % Allowed : 17.09 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.75 (0.31), residues: 638 helix: -3.65 (0.69), residues: 26 sheet: -0.75 (0.35), residues: 230 loop : -2.50 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.002 0.001 HIS B 82 PHE 0.010 0.001 PHE H 27 TYR 0.017 0.001 TYR H 116 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8693 (p0) cc_final: 0.8261 (p0) REVERT: A 442 ASP cc_start: 0.8064 (m-30) cc_final: 0.7802 (m-30) REVERT: B 3 GLN cc_start: 0.8159 (pp30) cc_final: 0.7812 (pp30) REVERT: C 18 ARG cc_start: 0.6929 (ttp80) cc_final: 0.6676 (ttp80) outliers start: 9 outliers final: 7 residues processed: 117 average time/residue: 0.2097 time to fit residues: 30.4564 Evaluate side-chains 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5209 Z= 0.218 Angle : 0.720 11.657 7075 Z= 0.372 Chirality : 0.045 0.173 747 Planarity : 0.005 0.047 906 Dihedral : 5.680 26.532 712 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.18 % Allowed : 19.09 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.72 (0.31), residues: 638 helix: -3.53 (0.70), residues: 27 sheet: -0.71 (0.35), residues: 230 loop : -2.50 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 83 HIS 0.002 0.001 HIS B 82 PHE 0.009 0.001 PHE B 64 TYR 0.012 0.001 TYR C 91 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8693 (p0) cc_final: 0.8288 (p0) REVERT: A 442 ASP cc_start: 0.8040 (m-30) cc_final: 0.7815 (m-30) REVERT: B 3 GLN cc_start: 0.8197 (pp30) cc_final: 0.7917 (pp30) REVERT: C 18 ARG cc_start: 0.6920 (ttp80) cc_final: 0.6663 (ttp80) REVERT: H 75 ASP cc_start: 0.8065 (t0) cc_final: 0.7850 (t0) REVERT: H 78 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8432 (pttm) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.2151 time to fit residues: 31.7545 Evaluate side-chains 117 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5209 Z= 0.305 Angle : 0.752 11.982 7075 Z= 0.391 Chirality : 0.046 0.169 747 Planarity : 0.005 0.046 906 Dihedral : 5.950 29.199 712 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 2.73 % Allowed : 19.82 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.31), residues: 638 helix: -3.39 (0.76), residues: 26 sheet: -0.77 (0.34), residues: 231 loop : -2.48 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS B 82 PHE 0.013 0.001 PHE L 71 TYR 0.018 0.001 TYR C 91 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8692 (p0) cc_final: 0.8281 (p0) REVERT: A 442 ASP cc_start: 0.8066 (m-30) cc_final: 0.7840 (m-30) REVERT: B 3 GLN cc_start: 0.8249 (pp30) cc_final: 0.7954 (pp30) REVERT: C 18 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6656 (ttp80) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.2353 time to fit residues: 34.2817 Evaluate side-chains 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 0.0570 chunk 52 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5209 Z= 0.200 Angle : 0.722 11.955 7075 Z= 0.374 Chirality : 0.045 0.141 747 Planarity : 0.005 0.047 906 Dihedral : 5.564 26.649 712 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.82 % Allowed : 21.09 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.55 (0.31), residues: 638 helix: -2.73 (0.95), residues: 20 sheet: -0.60 (0.36), residues: 219 loop : -2.41 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.008 0.001 PHE B 64 TYR 0.015 0.001 TYR A 369 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8591 (p0) cc_final: 0.8223 (p0) REVERT: A 442 ASP cc_start: 0.7971 (m-30) cc_final: 0.7754 (m-30) REVERT: C 18 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6690 (ttp80) outliers start: 10 outliers final: 10 residues processed: 116 average time/residue: 0.2148 time to fit residues: 30.5884 Evaluate side-chains 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5209 Z= 0.201 Angle : 0.737 12.564 7075 Z= 0.379 Chirality : 0.045 0.137 747 Planarity : 0.005 0.048 906 Dihedral : 5.399 26.722 712 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.82 % Allowed : 22.18 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.42 (0.31), residues: 638 helix: -2.61 (0.98), residues: 20 sheet: -0.50 (0.36), residues: 219 loop : -2.33 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.008 0.001 PHE B 64 TYR 0.014 0.001 TYR H 116 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8555 (p0) cc_final: 0.8250 (p0) REVERT: A 442 ASP cc_start: 0.7980 (m-30) cc_final: 0.7743 (m-30) REVERT: C 18 ARG cc_start: 0.6852 (ttp80) cc_final: 0.6612 (ttp80) REVERT: H 75 ASP cc_start: 0.8112 (t0) cc_final: 0.7887 (t0) REVERT: H 78 LYS cc_start: 0.8827 (pttm) cc_final: 0.8611 (pttm) outliers start: 10 outliers final: 10 residues processed: 118 average time/residue: 0.2213 time to fit residues: 32.0668 Evaluate side-chains 117 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5209 Z= 0.213 Angle : 0.740 10.496 7075 Z= 0.382 Chirality : 0.045 0.139 747 Planarity : 0.005 0.047 906 Dihedral : 5.374 26.359 712 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.00 % Allowed : 23.09 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.31), residues: 638 helix: -2.55 (0.99), residues: 20 sheet: -0.49 (0.36), residues: 220 loop : -2.33 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 83 HIS 0.002 0.001 HIS B 82 PHE 0.013 0.001 PHE B 32 TYR 0.015 0.001 TYR H 116 ARG 0.003 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8539 (p0) cc_final: 0.8245 (p0) REVERT: A 442 ASP cc_start: 0.7987 (m-30) cc_final: 0.7747 (m-30) REVERT: C 18 ARG cc_start: 0.6794 (ttp80) cc_final: 0.6564 (ttp80) REVERT: H 75 ASP cc_start: 0.8099 (t0) cc_final: 0.7853 (t0) REVERT: L 81 GLU cc_start: 0.7957 (pm20) cc_final: 0.7372 (pm20) outliers start: 11 outliers final: 11 residues processed: 115 average time/residue: 0.2064 time to fit residues: 29.2281 Evaluate side-chains 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 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 = 0.3684 r_free = 0.3684 target = 0.099381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077948 restraints weight = 13307.271| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.44 r_work: 0.3133 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5209 Z= 0.227 Angle : 0.748 11.624 7075 Z= 0.386 Chirality : 0.045 0.136 747 Planarity : 0.005 0.047 906 Dihedral : 5.369 26.252 712 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 2.00 % Allowed : 23.45 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -2.38 (0.31), residues: 638 helix: -2.50 (1.00), residues: 20 sheet: -0.51 (0.36), residues: 219 loop : -2.29 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 83 HIS 0.002 0.001 HIS B 82 PHE 0.014 0.001 PHE B 32 TYR 0.017 0.001 TYR H 116 ARG 0.003 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.33 seconds wall clock time: 33 minutes 6.25 seconds (1986.25 seconds total)