Starting phenix.real_space_refine on Tue Sep 24 03:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x96_33068/09_2024/7x96_33068_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x96_33068/09_2024/7x96_33068.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/7x96_33068/09_2024/7x96_33068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x96_33068/09_2024/7x96_33068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x96_33068/09_2024/7x96_33068_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x96_33068/09_2024/7x96_33068_trim.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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2159 2.51 5 N 556 2.21 5 O 670 1.98 5 H 3184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6586 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1826 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1624 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.60, per 1000 atoms: 0.55 Number of scatterers: 6586 At special positions: 0 Unit cell: (72.123, 86.216, 92.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 670 8.00 N 556 7.00 C 2159 6.00 H 3184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 543.8 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 14.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 4.481A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 389 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.922A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.581A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL H 116 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.677A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 2.25 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3183 1.03 - 1.23: 20 1.23 - 1.43: 1514 1.43 - 1.62: 1934 1.62 - 1.82: 21 Bond restraints: 6672 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11726 1.51 - 3.03: 178 3.03 - 4.54: 26 4.54 - 6.06: 7 6.06 - 7.57: 4 Bond angle restraints: 11941 Sorted by residual: angle pdb=" CA ARG L 97 " pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.21 106.93 3.28 1.13e+00 7.83e-01 8.43e+00 angle pdb=" C PRO L 96 " pdb=" N ARG L 97 " pdb=" CA ARG L 97 " ideal model delta sigma weight residual 122.30 125.62 -3.32 1.35e+00 5.49e-01 6.04e+00 angle pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " pdb=" CD ARG L 97 " ideal model delta sigma weight residual 111.30 116.67 -5.37 2.30e+00 1.89e-01 5.45e+00 angle pdb=" C3 MAN A 4 " pdb=" C2 MAN A 4 " pdb=" O2 MAN A 4 " ideal model delta sigma weight residual 111.77 105.58 6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 11936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 3063 21.62 - 43.23: 166 43.23 - 64.85: 57 64.85 - 86.47: 13 86.47 - 108.08: 5 Dihedral angle restraints: 3304 sinusoidal: 1796 harmonic: 1508 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.36 -88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 146.29 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 454 0.054 - 0.107: 55 0.107 - 0.161: 25 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 535 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2 BMA A 3 " pdb=" C1 BMA A 3 " pdb=" C3 BMA A 3 " pdb=" O2 BMA A 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE G 402 " pdb=" N ILE G 402 " pdb=" C ILE G 402 " pdb=" CB ILE G 402 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 532 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 97 " 0.199 9.50e-02 1.11e+02 6.65e-02 4.79e+00 pdb=" NE ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 97 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG L 97 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG L 97 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO G 521 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO L 96 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.015 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 288 2.17 - 2.78: 12644 2.78 - 3.38: 17363 3.38 - 3.99: 23147 3.99 - 4.60: 35239 Nonbonded interactions: 88681 Sorted by model distance: nonbonded pdb=" O TRP G 353 " pdb="HH12 ARG G 466 " model vdw 1.562 2.450 nonbonded pdb=" HG SER L 12 " pdb=" O ASP L 107 " model vdw 1.624 2.450 nonbonded pdb=" H LEU G 455 " pdb=" O PRO G 491 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLU H 89 " pdb=" H GLU H 89 " model vdw 1.649 2.450 ... (remaining 88676 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: 0.200 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.003 0.033 3488 Z= 0.201 Angle : 0.609 7.571 4747 Z= 0.300 Chirality : 0.045 0.268 535 Planarity : 0.005 0.086 603 Dihedral : 15.740 108.084 1322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.42), residues: 421 helix: -1.99 (1.15), residues: 19 sheet: -0.82 (0.42), residues: 167 loop : -0.77 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 99 PHE 0.005 0.001 PHE G 400 TYR 0.011 0.001 TYR H 80 ARG 0.005 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 493 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8639 (tp-100) REVERT: H 62 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3727 time to fit residues: 31.8115 Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3488 Z= 0.293 Angle : 0.548 4.868 4747 Z= 0.291 Chirality : 0.042 0.170 535 Planarity : 0.004 0.029 603 Dihedral : 10.703 79.020 582 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.09 % Allowed : 8.74 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.41), residues: 421 helix: -2.10 (1.11), residues: 20 sheet: -0.84 (0.43), residues: 155 loop : -0.97 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.010 0.001 TYR L 49 ARG 0.004 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8604 (tp-100) REVERT: H 62 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8394 (tm-30) REVERT: H 82 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7653 (tm-30) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.3732 time to fit residues: 28.0334 Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3488 Z= 0.220 Angle : 0.523 4.918 4747 Z= 0.271 Chirality : 0.042 0.156 535 Planarity : 0.004 0.028 603 Dihedral : 7.082 48.406 582 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.37 % Allowed : 7.65 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 421 helix: -2.07 (1.08), residues: 20 sheet: -0.59 (0.44), residues: 151 loop : -1.07 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 436 HIS 0.003 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.025 0.001 TYR L 49 ARG 0.003 0.000 ARG G 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8602 (tp-100) REVERT: H 62 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8402 (tm-30) REVERT: H 82 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.3704 time to fit residues: 28.2549 Evaluate side-chains 63 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3488 Z= 0.209 Angle : 0.511 4.967 4747 Z= 0.265 Chirality : 0.042 0.159 535 Planarity : 0.004 0.050 603 Dihedral : 5.870 46.927 582 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.64 % Allowed : 8.47 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.41), residues: 421 helix: -1.93 (1.13), residues: 20 sheet: -0.55 (0.44), residues: 152 loop : -1.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 436 HIS 0.002 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.027 0.001 TYR L 49 ARG 0.005 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8613 (tp-100) REVERT: H 62 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8417 (tm-30) REVERT: L 27 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8423 (tp40) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.3698 time to fit residues: 28.9955 Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3488 Z= 0.156 Angle : 0.504 5.196 4747 Z= 0.261 Chirality : 0.042 0.135 535 Planarity : 0.004 0.055 603 Dihedral : 5.726 46.901 582 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.09 % Allowed : 10.11 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.41), residues: 421 helix: -1.83 (1.12), residues: 20 sheet: -0.43 (0.44), residues: 152 loop : -0.89 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 436 HIS 0.002 0.001 HIS L 90 PHE 0.005 0.001 PHE G 347 TYR 0.024 0.001 TYR L 49 ARG 0.007 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8420 (tm-30) REVERT: L 27 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8405 (tp40) REVERT: L 55 GLU cc_start: 0.9287 (tp30) cc_final: 0.9051 (tp30) outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.3621 time to fit residues: 28.1286 Evaluate side-chains 62 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3488 Z= 0.181 Angle : 0.503 5.071 4747 Z= 0.262 Chirality : 0.042 0.135 535 Planarity : 0.004 0.049 603 Dihedral : 5.496 46.740 582 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.37 % Allowed : 10.93 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.42), residues: 421 helix: -1.73 (1.14), residues: 20 sheet: -0.51 (0.44), residues: 155 loop : -0.78 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.007 0.001 PHE H 64 TYR 0.024 0.001 TYR L 49 ARG 0.007 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8491 (tp-100) REVERT: H 62 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8421 (tm-30) REVERT: L 27 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8400 (tp40) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.3024 time to fit residues: 23.0706 Evaluate side-chains 62 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3488 Z= 0.156 Angle : 0.500 5.228 4747 Z= 0.261 Chirality : 0.042 0.136 535 Planarity : 0.004 0.040 603 Dihedral : 5.265 46.518 582 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.64 % Allowed : 12.02 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.42), residues: 421 helix: -1.59 (1.22), residues: 20 sheet: -0.32 (0.45), residues: 152 loop : -0.75 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.005 0.001 PHE H 64 TYR 0.027 0.001 TYR L 49 ARG 0.005 0.001 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8470 (tp-100) REVERT: H 62 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8401 (tm-30) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.3212 time to fit residues: 25.5802 Evaluate side-chains 63 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3488 Z= 0.176 Angle : 0.498 5.108 4747 Z= 0.261 Chirality : 0.041 0.135 535 Planarity : 0.004 0.035 603 Dihedral : 5.155 46.697 582 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.64 % Allowed : 11.75 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.42), residues: 421 helix: -1.51 (1.20), residues: 20 sheet: -0.30 (0.45), residues: 151 loop : -0.80 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.023 0.001 TYR L 49 ARG 0.005 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 378 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8620 (ptmm) REVERT: G 414 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8486 (tp-100) REVERT: H 62 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8398 (tm-30) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.3016 time to fit residues: 22.4479 Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3488 Z= 0.219 Angle : 0.509 4.923 4747 Z= 0.267 Chirality : 0.041 0.137 535 Planarity : 0.004 0.036 603 Dihedral : 5.077 46.622 582 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.64 % Allowed : 12.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.42), residues: 421 helix: -1.64 (1.23), residues: 20 sheet: -0.29 (0.45), residues: 151 loop : -0.79 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.006 0.001 PHE G 429 TYR 0.024 0.001 TYR L 49 ARG 0.005 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 378 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8603 (ptmm) REVERT: G 414 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8495 (tp-100) REVERT: H 62 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8383 (tm-30) REVERT: L 27 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8413 (tp40) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.2936 time to fit residues: 21.9520 Evaluate side-chains 63 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3488 Z= 0.160 Angle : 0.500 5.208 4747 Z= 0.260 Chirality : 0.043 0.196 535 Planarity : 0.004 0.038 603 Dihedral : 4.976 46.973 582 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.64 % Allowed : 11.48 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.90 (0.42), residues: 421 helix: -1.41 (1.24), residues: 20 sheet: -0.22 (0.45), residues: 151 loop : -0.73 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.010 0.001 PHE H 64 TYR 0.024 0.001 TYR L 49 ARG 0.005 0.000 ARG L 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 378 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8602 (ptmm) REVERT: G 414 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8478 (tp-100) REVERT: H 62 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8385 (tm-30) REVERT: L 108 ILE cc_start: 0.9107 (pt) cc_final: 0.8799 (pt) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.3082 time to fit residues: 23.9028 Evaluate side-chains 64 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.050272 restraints weight = 33013.814| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.24 r_work: 0.2652 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3488 Z= 0.146 Angle : 0.501 5.301 4747 Z= 0.261 Chirality : 0.042 0.137 535 Planarity : 0.004 0.037 603 Dihedral : 4.860 46.443 582 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.64 % Allowed : 12.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.88 (0.42), residues: 421 helix: -1.53 (1.23), residues: 20 sheet: -0.21 (0.45), residues: 151 loop : -0.70 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.005 0.001 PHE G 400 TYR 0.023 0.001 TYR L 49 ARG 0.004 0.000 ARG H 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.99 seconds wall clock time: 41 minutes 30.28 seconds (2490.28 seconds total)