Starting phenix.real_space_refine on Thu Nov 14 02:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3u_35156/11_2024/8i3u_35156.cif" } resolution = 3.6 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= 0.036 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 16 5.16 5 C 2161 2.51 5 N 579 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} 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: 3.34, per 1000 atoms: 0.98 Number of scatterers: 3408 At special positions: 0 Unit cell: (63.65, 61.75, 106.4, 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 16 16.00 O 652 8.00 N 579 7.00 C 2161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " 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 92 " distance=2.39 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 474.4 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.575A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.117A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.339A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.644A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N ILE H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.525A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 255 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: 0.87 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1100 1.34 - 1.46: 903 1.46 - 1.58: 1473 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3496 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.90e-01 ... (remaining 3491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 4629 1.35 - 2.71: 89 2.71 - 4.06: 22 4.06 - 5.41: 8 5.41 - 6.76: 1 Bond angle restraints: 4749 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 113.08 6.76 1.25e+00 6.40e-01 2.93e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.84e+00 angle pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" ideal model delta sigma weight residual 117.93 120.61 -2.68 1.20e+00 6.94e-01 4.98e+00 angle pdb=" C VAL H 48 " pdb=" N SER H 49 " pdb=" CA SER H 49 " ideal model delta sigma weight residual 122.21 118.76 3.45 1.62e+00 3.81e-01 4.53e+00 angle pdb=" C GLY A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta sigma weight residual 121.54 125.09 -3.55 1.91e+00 2.74e-01 3.46e+00 ... (remaining 4744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1865 11.54 - 23.08: 136 23.08 - 34.61: 46 34.61 - 46.15: 10 46.15 - 57.69: 2 Dihedral angle restraints: 2059 sinusoidal: 812 harmonic: 1247 Sorted by residual: dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+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 93.00 118.67 -25.67 1 1.00e+01 1.00e-02 9.48e+00 ... (remaining 2056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 301 0.027 - 0.053: 126 0.053 - 0.080: 29 0.080 - 0.106: 37 0.106 - 0.132: 12 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA GLU H 26 " pdb=" N GLU H 26 " pdb=" C GLU H 26 " pdb=" CB GLU H 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 502 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO L 95A" 0.152 5.00e-02 4.00e+02 pdb=" CA PRO L 95A" -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 95A" -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO A 491 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.015 5.00e-02 4.00e+02 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 221 2.74 - 3.28: 3219 3.28 - 3.82: 5418 3.82 - 4.36: 6360 4.36 - 4.90: 11589 Nonbonded interactions: 26807 Sorted by model distance: nonbonded pdb=" O HIS L 49 " pdb=" OG1 THR L 53 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.268 3.040 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP H 31 " model vdw 2.289 3.120 nonbonded pdb=" O ILE H 29 " pdb=" NH2 ARG H 71 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.319 3.120 ... (remaining 26802 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.002 0.041 3496 Z= 0.165 Angle : 0.535 6.765 4749 Z= 0.299 Chirality : 0.041 0.132 505 Planarity : 0.005 0.088 620 Dihedral : 9.198 57.687 1258 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.09 % Allowed : 5.72 % Favored : 93.19 % 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: -0.52 (0.41), residues: 431 helix: -1.62 (0.94), residues: 27 sheet: 0.02 (0.46), residues: 132 loop : -0.34 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE A 456 TYR 0.011 0.001 TYR L 91 ARG 0.001 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.476 Fit side-chains REVERT: A 392 PHE cc_start: 0.7569 (m-80) cc_final: 0.7264 (m-80) REVERT: A 444 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8073 (mtmm) REVERT: H 34 MET cc_start: 0.8171 (mmm) cc_final: 0.7867 (mmm) REVERT: L 29 ILE cc_start: 0.7289 (mm) cc_final: 0.7057 (mm) outliers start: 4 outliers final: 0 residues processed: 115 average time/residue: 0.1839 time to fit residues: 24.9073 Evaluate side-chains 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN L 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3496 Z= 0.346 Angle : 0.631 8.634 4749 Z= 0.323 Chirality : 0.043 0.158 505 Planarity : 0.006 0.092 620 Dihedral : 5.110 26.581 505 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.54 % Allowed : 14.99 % Favored : 81.47 % 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: -0.61 (0.41), residues: 431 helix: -1.35 (1.00), residues: 28 sheet: 0.07 (0.48), residues: 124 loop : -0.49 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE A 342 TYR 0.020 0.002 TYR L 91 ARG 0.005 0.001 ARG H 100J *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.410 Fit side-chains REVERT: A 365 TYR cc_start: 0.8198 (m-80) cc_final: 0.7910 (m-80) REVERT: A 403 ARG cc_start: 0.8278 (ptm160) cc_final: 0.8077 (ptm160) REVERT: A 444 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8072 (mtmm) REVERT: H 34 MET cc_start: 0.8087 (mmm) cc_final: 0.7806 (mmm) REVERT: H 108 MET cc_start: 0.8334 (tpp) cc_final: 0.8106 (tpp) REVERT: L 107 LYS cc_start: 0.8172 (tmtt) cc_final: 0.7856 (mmtm) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1880 time to fit residues: 21.6471 Evaluate side-chains 92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3496 Z= 0.242 Angle : 0.586 8.438 4749 Z= 0.294 Chirality : 0.042 0.146 505 Planarity : 0.005 0.084 620 Dihedral : 4.797 22.169 505 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.09 % Allowed : 16.62 % Favored : 79.29 % 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: -0.53 (0.41), residues: 431 helix: -1.32 (1.01), residues: 28 sheet: 0.23 (0.47), residues: 130 loop : -0.50 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.015 0.001 TYR L 91 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.386 Fit side-chains REVERT: A 365 TYR cc_start: 0.8258 (m-80) cc_final: 0.7950 (m-80) REVERT: H 34 MET cc_start: 0.8038 (mmm) cc_final: 0.7776 (mmm) REVERT: L 107 LYS cc_start: 0.8359 (tmtt) cc_final: 0.8097 (mmtm) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.2109 time to fit residues: 21.9065 Evaluate side-chains 88 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3496 Z= 0.246 Angle : 0.598 8.580 4749 Z= 0.294 Chirality : 0.042 0.146 505 Planarity : 0.006 0.091 620 Dihedral : 4.754 24.456 505 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.09 % Allowed : 17.71 % Favored : 78.20 % 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: -0.58 (0.42), residues: 431 helix: -1.26 (1.02), residues: 28 sheet: 0.17 (0.47), residues: 133 loop : -0.54 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.011 0.001 TYR L 91 ARG 0.005 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.405 Fit side-chains REVERT: A 365 TYR cc_start: 0.8282 (m-80) cc_final: 0.7883 (m-80) REVERT: A 468 ILE cc_start: 0.9125 (pt) cc_final: 0.8758 (mt) REVERT: H 34 MET cc_start: 0.8096 (mmm) cc_final: 0.7846 (mmm) REVERT: H 75 LYS cc_start: 0.8979 (tptm) cc_final: 0.8710 (mptt) REVERT: L 107 LYS cc_start: 0.8283 (tmtt) cc_final: 0.8082 (mmtm) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.1849 time to fit residues: 18.8744 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3496 Z= 0.227 Angle : 0.574 9.548 4749 Z= 0.281 Chirality : 0.042 0.144 505 Planarity : 0.005 0.088 620 Dihedral : 4.628 22.619 505 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.81 % Allowed : 20.44 % Favored : 75.75 % 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: -0.54 (0.42), residues: 431 helix: -1.21 (1.05), residues: 28 sheet: 0.19 (0.47), residues: 133 loop : -0.52 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.009 0.001 TYR A 453 ARG 0.004 0.000 ARG H 100J *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.392 Fit side-chains REVERT: A 365 TYR cc_start: 0.8303 (m-80) cc_final: 0.7831 (m-80) REVERT: A 468 ILE cc_start: 0.9113 (pt) cc_final: 0.8784 (mt) REVERT: H 34 MET cc_start: 0.8097 (mmm) cc_final: 0.7794 (mmm) REVERT: H 75 LYS cc_start: 0.8990 (tptm) cc_final: 0.8643 (mmmt) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.2094 time to fit residues: 21.4137 Evaluate side-chains 83 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3496 Z= 0.261 Angle : 0.607 9.580 4749 Z= 0.296 Chirality : 0.042 0.145 505 Planarity : 0.006 0.093 620 Dihedral : 4.761 23.942 505 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.81 % Allowed : 20.71 % Favored : 75.48 % 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: -0.57 (0.42), residues: 431 helix: -1.11 (1.07), residues: 28 sheet: 0.15 (0.47), residues: 133 loop : -0.54 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.010 0.001 TYR L 91 ARG 0.004 0.000 ARG H 100J *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.385 Fit side-chains REVERT: A 365 TYR cc_start: 0.8355 (m-80) cc_final: 0.7829 (m-80) REVERT: A 468 ILE cc_start: 0.9126 (pt) cc_final: 0.8786 (mt) REVERT: H 34 MET cc_start: 0.8033 (mmm) cc_final: 0.7693 (mmm) REVERT: H 75 LYS cc_start: 0.8993 (tptm) cc_final: 0.8641 (mmmt) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1774 time to fit residues: 18.7224 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3496 Z= 0.347 Angle : 0.642 10.820 4749 Z= 0.316 Chirality : 0.043 0.150 505 Planarity : 0.006 0.091 620 Dihedral : 5.022 22.909 505 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.09 % Allowed : 20.16 % Favored : 75.75 % 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: -0.74 (0.41), residues: 431 helix: -1.18 (1.06), residues: 28 sheet: 0.19 (0.49), residues: 122 loop : -0.73 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.012 0.002 TYR L 91 ARG 0.004 0.001 ARG H 100J *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.403 Fit side-chains REVERT: A 365 TYR cc_start: 0.8400 (m-80) cc_final: 0.7869 (m-80) REVERT: A 468 ILE cc_start: 0.9125 (pt) cc_final: 0.8765 (mt) REVERT: H 34 MET cc_start: 0.7987 (mmm) cc_final: 0.7617 (mmm) REVERT: H 75 LYS cc_start: 0.9014 (tptm) cc_final: 0.8690 (mmmt) REVERT: H 108 MET cc_start: 0.8368 (tpp) cc_final: 0.8117 (tpp) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1884 time to fit residues: 20.0614 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 36 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3496 Z= 0.228 Angle : 0.607 9.907 4749 Z= 0.293 Chirality : 0.042 0.143 505 Planarity : 0.005 0.090 620 Dihedral : 4.744 23.857 505 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.27 % Allowed : 22.34 % Favored : 74.39 % 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: -0.61 (0.42), residues: 431 helix: -1.06 (1.09), residues: 28 sheet: 0.25 (0.47), residues: 131 loop : -0.65 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.009 0.001 PHE H 27 TYR 0.010 0.001 TYR L 91 ARG 0.005 0.000 ARG H 100J *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.361 Fit side-chains REVERT: A 365 TYR cc_start: 0.8353 (m-80) cc_final: 0.7867 (m-80) REVERT: A 468 ILE cc_start: 0.9107 (pt) cc_final: 0.8823 (mt) REVERT: H 34 MET cc_start: 0.8024 (mmm) cc_final: 0.7697 (mmm) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.1738 time to fit residues: 18.3896 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3496 Z= 0.287 Angle : 0.637 10.192 4749 Z= 0.313 Chirality : 0.043 0.146 505 Planarity : 0.006 0.091 620 Dihedral : 4.863 23.739 505 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.09 % Allowed : 22.07 % Favored : 73.84 % 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: -0.64 (0.41), residues: 431 helix: -1.10 (1.08), residues: 28 sheet: 0.28 (0.47), residues: 129 loop : -0.68 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.009 0.001 TYR A 453 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.374 Fit side-chains REVERT: A 365 TYR cc_start: 0.8401 (m-80) cc_final: 0.7912 (m-80) REVERT: A 468 ILE cc_start: 0.9119 (pt) cc_final: 0.8817 (mt) REVERT: H 34 MET cc_start: 0.8004 (mmm) cc_final: 0.7671 (mmm) REVERT: H 76 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8788 (m110) REVERT: H 108 MET cc_start: 0.8344 (tpp) cc_final: 0.8088 (tpp) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.1746 time to fit residues: 18.2741 Evaluate side-chains 91 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3496 Z= 0.257 Angle : 0.642 10.133 4749 Z= 0.313 Chirality : 0.042 0.145 505 Planarity : 0.006 0.090 620 Dihedral : 4.802 23.653 505 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.00 % Allowed : 23.16 % Favored : 73.84 % 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: -0.60 (0.41), residues: 431 helix: -1.07 (1.07), residues: 28 sheet: 0.28 (0.47), residues: 129 loop : -0.65 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.009 0.001 TYR L 91 ARG 0.005 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.338 Fit side-chains REVERT: A 365 TYR cc_start: 0.8374 (m-80) cc_final: 0.7893 (m-80) REVERT: A 468 ILE cc_start: 0.9136 (pt) cc_final: 0.8852 (mt) REVERT: H 34 MET cc_start: 0.7966 (mmm) cc_final: 0.7606 (mmm) REVERT: H 108 MET cc_start: 0.8363 (tpp) cc_final: 0.8101 (tpp) REVERT: L 6 GLN cc_start: 0.6739 (mt0) cc_final: 0.6465 (tt0) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1816 time to fit residues: 18.2864 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 0.0060 chunk 24 optimal weight: 0.0070 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 41 optimal weight: 0.0170 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132054 restraints weight = 4527.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135810 restraints weight = 2698.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138308 restraints weight = 1935.774| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3496 Z= 0.168 Angle : 0.583 9.683 4749 Z= 0.286 Chirality : 0.042 0.125 505 Planarity : 0.005 0.090 620 Dihedral : 4.253 23.710 505 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.36 % Allowed : 24.25 % Favored : 74.39 % 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: -0.37 (0.42), residues: 431 helix: -0.87 (1.14), residues: 28 sheet: 0.40 (0.47), residues: 131 loop : -0.47 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.006 0.002 HIS H 35 PHE 0.008 0.001 PHE H 27 TYR 0.009 0.001 TYR A 453 ARG 0.005 0.001 ARG H 100J Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1437.76 seconds wall clock time: 26 minutes 36.11 seconds (1596.11 seconds total)