Starting phenix.real_space_refine on Mon Sep 23 14:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/09_2024/7k9i_22749.cif" } resolution = 3.3 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= 0.002 sd= 0.053 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 14 5.16 5 C 2095 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 3295 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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: 3.06, per 1000 atoms: 0.93 Number of scatterers: 3295 At special positions: 0 Unit cell: (64.9, 85.8, 86.9, 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 14 16.00 O 632 8.00 N 554 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 443.5 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.605A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.896A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.277A 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 'H' and resid 86 through 90 removed outlier: 3.569A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.306A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.846A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.92 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: 1051 1.34 - 1.47: 910 1.47 - 1.59: 1402 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3379 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.340 1.269 0.071 5.87e-02 2.90e+02 1.47e+00 bond pdb=" CB ASN L 36 " pdb=" CG ASN L 36 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ILE A 434 " pdb=" CG2 ILE A 434 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.69e-01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4390 1.51 - 3.01: 171 3.01 - 4.52: 31 4.52 - 6.03: 6 6.03 - 7.54: 3 Bond angle restraints: 4601 Sorted by residual: angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N CYS H 95 " pdb=" CA CYS H 95 " pdb=" C CYS H 95 " ideal model delta sigma weight residual 110.32 106.37 3.95 1.59e+00 3.96e-01 6.17e+00 angle pdb=" CA GLU A 516 " pdb=" CB GLU A 516 " pdb=" CG GLU A 516 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.23e+00 angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 angle pdb=" N GLY L 70 " pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 112.10 108.16 3.94 1.82e+00 3.02e-01 4.68e+00 ... (remaining 4596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1821 17.83 - 35.66: 139 35.66 - 53.48: 17 53.48 - 71.31: 4 71.31 - 89.14: 2 Dihedral angle restraints: 1983 sinusoidal: 770 harmonic: 1213 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+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 93.00 129.94 -36.94 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 317 0.039 - 0.078: 118 0.078 - 0.116: 59 0.116 - 0.155: 8 0.155 - 0.193: 1 Chirality restraints: 503 Sorted by residual: 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 2.36 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE L 87 " pdb=" N ILE L 87 " pdb=" C ILE L 87 " pdb=" CB ILE L 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 500 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.073 9.50e-02 1.11e+02 4.13e-02 8.64e+00 pdb=" NE ARG A 355 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO L 42 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 463 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.019 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 72 2.67 - 3.23: 3219 3.23 - 3.79: 4886 3.79 - 4.34: 6660 4.34 - 4.90: 11314 Nonbonded interactions: 26151 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.118 3.040 nonbonded pdb=" O ILE H 30 " pdb=" OG1 THR H 53 " model vdw 2.140 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.173 3.120 nonbonded pdb=" OG1 THR L 12 " pdb=" O GLU L 16 " model vdw 2.189 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.239 3.040 ... (remaining 26146 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: 1.140 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.071 3379 Z= 0.361 Angle : 0.719 7.536 4601 Z= 0.385 Chirality : 0.049 0.193 503 Planarity : 0.005 0.043 591 Dihedral : 12.862 89.140 1199 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 417 helix: -1.66 (0.85), residues: 32 sheet: 0.51 (0.45), residues: 133 loop : -1.05 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.012 0.002 PHE A 490 TYR 0.015 0.001 TYR A 380 ARG 0.049 0.003 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7615 (pt0) cc_final: 0.7371 (pt0) REVERT: H 108 ASP cc_start: 0.7834 (t0) cc_final: 0.7624 (t0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2355 time to fit residues: 17.5415 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3379 Z= 0.195 Angle : 0.678 6.856 4601 Z= 0.352 Chirality : 0.047 0.134 503 Planarity : 0.005 0.040 591 Dihedral : 6.503 54.734 485 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 13.52 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.41), residues: 417 helix: -1.31 (0.97), residues: 33 sheet: 0.13 (0.44), residues: 142 loop : -0.73 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.008 0.001 TYR A 451 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8473 (tppt) REVERT: A 420 ASP cc_start: 0.8260 (m-30) cc_final: 0.7715 (m-30) REVERT: H 108 ASP cc_start: 0.7651 (t0) cc_final: 0.7378 (t0) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.1840 time to fit residues: 15.8311 Evaluate side-chains 67 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3379 Z= 0.205 Angle : 0.649 6.451 4601 Z= 0.333 Chirality : 0.045 0.153 503 Planarity : 0.004 0.038 591 Dihedral : 6.245 54.842 485 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.97 % Allowed : 17.46 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.40), residues: 417 helix: -1.18 (1.13), residues: 26 sheet: 0.20 (0.43), residues: 142 loop : -0.80 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE A 490 TYR 0.011 0.001 TYR A 380 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.393 Fit side-chains REVERT: A 417 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8489 (tppt) REVERT: A 420 ASP cc_start: 0.8244 (m-30) cc_final: 0.7746 (m-30) REVERT: H 16 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: H 66 ARG cc_start: 0.6682 (mpp-170) cc_final: 0.6436 (mpp-170) REVERT: H 108 ASP cc_start: 0.7695 (t0) cc_final: 0.7468 (t0) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1960 time to fit residues: 17.3245 Evaluate side-chains 63 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3379 Z= 0.262 Angle : 0.641 7.453 4601 Z= 0.329 Chirality : 0.045 0.130 503 Planarity : 0.005 0.039 591 Dihedral : 6.269 54.604 485 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.66 % Allowed : 17.75 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.40), residues: 417 helix: -1.20 (1.12), residues: 26 sheet: 0.22 (0.43), residues: 142 loop : -0.85 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS L 97 PHE 0.010 0.001 PHE A 490 TYR 0.012 0.001 TYR A 380 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8486 (tppt) REVERT: A 420 ASP cc_start: 0.8245 (m-30) cc_final: 0.7749 (m-30) REVERT: H 16 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: H 108 ASP cc_start: 0.7855 (t0) cc_final: 0.7528 (t0) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.1717 time to fit residues: 15.2403 Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3379 Z= 0.188 Angle : 0.620 6.121 4601 Z= 0.320 Chirality : 0.045 0.132 503 Planarity : 0.004 0.039 591 Dihedral : 6.127 54.118 485 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.23 % Allowed : 18.31 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.40), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.07 (0.43), residues: 145 loop : -0.72 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.007 0.001 PHE A 490 TYR 0.015 0.001 TYR A 451 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8414 (tppt) REVERT: A 420 ASP cc_start: 0.8246 (m-30) cc_final: 0.7767 (m-30) REVERT: H 18 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6812 (mm) REVERT: H 66 ARG cc_start: 0.6652 (mpp-170) cc_final: 0.6441 (mpp-170) REVERT: H 108 ASP cc_start: 0.7796 (t0) cc_final: 0.7459 (t0) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.2038 time to fit residues: 20.1567 Evaluate side-chains 78 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3379 Z= 0.171 Angle : 0.626 7.386 4601 Z= 0.318 Chirality : 0.045 0.140 503 Planarity : 0.004 0.038 591 Dihedral : 6.038 54.326 485 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.38 % Allowed : 19.72 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.40), residues: 417 helix: -2.15 (0.84), residues: 33 sheet: 0.06 (0.46), residues: 130 loop : -0.71 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.012 0.001 TYR A 451 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7749 (mp10) cc_final: 0.7523 (mp10) REVERT: A 417 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8403 (tppt) REVERT: A 420 ASP cc_start: 0.8185 (m-30) cc_final: 0.7717 (m-30) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.1890 time to fit residues: 17.6791 Evaluate side-chains 72 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3379 Z= 0.171 Angle : 0.612 6.854 4601 Z= 0.311 Chirality : 0.045 0.142 503 Planarity : 0.004 0.037 591 Dihedral : 5.952 54.184 485 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.79 % Allowed : 19.15 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.41), residues: 417 helix: -1.54 (1.01), residues: 27 sheet: 0.23 (0.45), residues: 134 loop : -0.62 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.007 0.001 TYR A 380 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8351 (tppt) REVERT: A 420 ASP cc_start: 0.8143 (m-30) cc_final: 0.7654 (m-30) REVERT: A 517 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8145 (tt) REVERT: L 39 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7511 (tm-30) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1626 time to fit residues: 16.0949 Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.005 0.068 3379 Z= 0.339 Angle : 0.700 8.163 4601 Z= 0.359 Chirality : 0.047 0.143 503 Planarity : 0.005 0.042 591 Dihedral : 6.318 54.210 485 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.66 % Allowed : 20.56 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.40), residues: 417 helix: -1.58 (0.99), residues: 27 sheet: 0.20 (0.44), residues: 131 loop : -0.78 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS L 97 PHE 0.012 0.001 PHE A 490 TYR 0.013 0.001 TYR A 380 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8406 (tppt) REVERT: A 420 ASP cc_start: 0.8267 (m-30) cc_final: 0.7803 (m-30) REVERT: A 517 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8170 (tt) REVERT: H 3 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7914 (tm-30) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.1701 time to fit residues: 16.1032 Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3379 Z= 0.182 Angle : 0.668 8.216 4601 Z= 0.336 Chirality : 0.045 0.139 503 Planarity : 0.005 0.043 591 Dihedral : 6.084 54.366 485 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.94 % Allowed : 20.85 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.40), residues: 417 helix: -2.03 (0.86), residues: 33 sheet: -0.14 (0.46), residues: 130 loop : -0.69 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 400 TYR 0.016 0.001 TYR A 451 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8356 (tppt) REVERT: A 420 ASP cc_start: 0.8228 (m-30) cc_final: 0.7761 (m-30) REVERT: A 517 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8213 (tt) REVERT: H 107 MET cc_start: 0.8572 (mpp) cc_final: 0.8040 (mpp) outliers start: 14 outliers final: 13 residues processed: 79 average time/residue: 0.1659 time to fit residues: 15.8977 Evaluate side-chains 79 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.0060 overall best weight: 1.1298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3379 Z= 0.218 Angle : 0.672 8.078 4601 Z= 0.338 Chirality : 0.046 0.143 503 Planarity : 0.005 0.044 591 Dihedral : 6.097 54.469 485 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.66 % Allowed : 21.69 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.40), residues: 417 helix: -2.06 (0.86), residues: 33 sheet: -0.16 (0.46), residues: 130 loop : -0.67 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS L 97 PHE 0.006 0.001 PHE A 490 TYR 0.016 0.001 TYR A 451 ARG 0.006 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7546 (mp10) cc_final: 0.7338 (mp10) REVERT: A 417 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8365 (tppt) REVERT: A 420 ASP cc_start: 0.8241 (m-30) cc_final: 0.7781 (m-30) REVERT: A 517 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8195 (tt) REVERT: H 107 MET cc_start: 0.8574 (mpp) cc_final: 0.8016 (mpp) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.1573 time to fit residues: 14.4286 Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 39 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.094520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079110 restraints weight = 8020.890| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.30 r_work: 0.3244 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3379 Z= 0.171 Angle : 0.650 8.024 4601 Z= 0.325 Chirality : 0.045 0.131 503 Planarity : 0.005 0.041 591 Dihedral : 5.927 54.578 485 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.10 % Allowed : 21.97 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.41), residues: 417 helix: -2.12 (0.85), residues: 33 sheet: -0.15 (0.45), residues: 130 loop : -0.59 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.005 0.001 PHE A 400 TYR 0.012 0.001 TYR A 451 ARG 0.007 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.32 seconds wall clock time: 23 minutes 16.31 seconds (1396.31 seconds total)