Starting phenix.real_space_refine on Sun Mar 10 16:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsc_32753/03_2024/7wsc_32753.pdb" } resolution = 3.78 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= 0.019 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 15 5.16 5 C 2156 2.51 5 N 563 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 340": "OE1" <-> "OE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 405": "OD1" <-> "OD2" Residue "R ASP 442": "OD1" <-> "OD2" Residue "R TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 493": "NH1" <-> "NH2" Residue "R TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "L GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3369 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.45, per 1000 atoms: 0.73 Number of scatterers: 3369 At special positions: 0 Unit cell: (63.13, 87.74, 74.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 635 8.00 N 563 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.01 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 666.0 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 364 through 369 removed outlier: 3.593A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 4.117A pdb=" N ASN R 388 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.870A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O VAL H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'L' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.915A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.861A pdb=" N LEU H 37 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70 removed outlier: 6.433A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 144 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.736A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.554A pdb=" N ILE L 109 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 183 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: 0.79 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 532 1.26 - 1.40: 979 1.40 - 1.54: 1912 1.54 - 1.68: 17 1.68 - 1.82: 18 Bond restraints: 3458 Sorted by residual: bond pdb=" CA TYR R 380 " pdb=" C TYR R 380 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.35e-02 5.49e+03 9.08e+01 bond pdb=" C PHE R 377 " pdb=" O PHE R 377 " ideal model delta sigma weight residual 1.235 1.116 0.120 1.26e-02 6.30e+03 9.01e+01 bond pdb=" C VAL R 382 " pdb=" O VAL R 382 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.03e-02 9.43e+03 6.47e+01 bond pdb=" CB TYR R 380 " pdb=" CG TYR R 380 " ideal model delta sigma weight residual 1.512 1.341 0.171 2.20e-02 2.07e+03 6.07e+01 bond pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 1.523 1.436 0.088 1.25e-02 6.40e+03 4.91e+01 ... (remaining 3453 not shown) Histogram of bond angle deviations from ideal: 85.51 - 95.23: 5 95.23 - 104.95: 78 104.95 - 114.66: 1901 114.66 - 124.38: 2603 124.38 - 134.10: 108 Bond angle restraints: 4695 Sorted by residual: angle pdb=" N GLY R 482 " pdb=" CA GLY R 482 " pdb=" C GLY R 482 " ideal model delta sigma weight residual 113.18 85.51 27.67 2.37e+00 1.78e-01 1.36e+02 angle pdb=" C PHE R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.84 132.96 -13.12 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N PHE R 486 " pdb=" CA PHE R 486 " pdb=" C PHE R 486 " ideal model delta sigma weight residual 111.04 95.20 15.84 1.55e+00 4.16e-01 1.04e+02 angle pdb=" N ALA R 475 " pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 107.98 89.55 18.43 1.88e+00 2.83e-01 9.61e+01 angle pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" CD PRO L 37 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 4690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1778 15.87 - 31.73: 183 31.73 - 47.60: 60 47.60 - 63.46: 15 63.46 - 79.32: 8 Dihedral angle restraints: 2044 sinusoidal: 827 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.68 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N CYS R 488 " pdb=" C CYS R 488 " pdb=" CA CYS R 488 " pdb=" CB CYS R 488 " ideal model delta harmonic sigma weight residual 122.80 106.51 16.29 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ARG H 71 " pdb=" C ARG H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 2041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 476 0.158 - 0.317: 11 0.317 - 0.475: 6 0.475 - 0.633: 4 0.633 - 0.791: 2 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA CYS R 379 " pdb=" N CYS R 379 " pdb=" C CYS R 379 " pdb=" CB CYS R 379 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN R 477 " pdb=" N ASN R 477 " pdb=" C ASN R 477 " pdb=" CB ASN R 477 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 496 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.119 5.00e-02 4.00e+02 1.69e-01 4.60e+01 pdb=" N PRO R 491 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 368 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU R 368 " 0.111 2.00e-02 2.50e+03 pdb=" O LEU R 368 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR R 369 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 477 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASN R 477 " -0.110 2.00e-02 2.50e+03 pdb=" O ASN R 477 " 0.043 2.00e-02 2.50e+03 pdb=" N LYS R 478 " 0.035 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 1670 2.92 - 3.58: 4936 3.58 - 4.24: 7946 4.24 - 4.90: 13267 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" O TYR R 473 " pdb=" O CYS R 488 " model vdw 1.600 3.040 nonbonded pdb=" OG1 THR L 33 " pdb=" OE2 GLU L 36 " model vdw 2.071 2.440 nonbonded pdb=" O ASN R 477 " pdb=" ND2 ASN R 477 " model vdw 2.084 2.520 nonbonded pdb=" OG SER H 36 " pdb=" O MET H 102 " model vdw 2.088 2.440 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.118 2.440 ... (remaining 27823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.490 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.510 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.013 0.171 3458 Z= 0.821 Angle : 1.667 30.153 4695 Z= 0.880 Chirality : 0.101 0.791 499 Planarity : 0.012 0.169 604 Dihedral : 15.341 79.299 1263 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 41.09 Ramachandran Plot: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.64 % Rotamer: Outliers : 4.99 % Allowed : 1.94 % Favored : 93.07 % Cbeta Deviations : 1.31 % Peptide Plane: Cis-proline : 10.00 % 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: -4.09 (0.39), residues: 414 helix: -5.03 (0.30), residues: 12 sheet: -2.57 (0.41), residues: 129 loop : -2.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 PHE 0.056 0.004 PHE R 490 TYR 0.023 0.002 TYR H 51 ARG 0.039 0.002 ARG R 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.392 Fit side-chains REVERT: R 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 423 TYR cc_start: 0.7992 (t80) cc_final: 0.7695 (t80) REVERT: R 455 LEU cc_start: 0.7505 (pt) cc_final: 0.7293 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6242 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7557 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7213 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7826 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.1536 time to fit residues: 24.2829 Evaluate side-chains 103 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 474 GLN Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 486 PHE Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain L residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 3458 Z= 0.355 Angle : 0.934 13.471 4695 Z= 0.461 Chirality : 0.054 0.296 499 Planarity : 0.010 0.148 604 Dihedral : 9.952 85.956 542 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.97 % Allowed : 12.80 % Favored : 86.23 % Rotamer: Outliers : 6.37 % Allowed : 16.34 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.56 (0.40), residues: 414 helix: -3.06 (1.14), residues: 12 sheet: -2.43 (0.41), residues: 128 loop : -2.41 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 59 HIS 0.008 0.003 HIS H 54 PHE 0.016 0.002 PHE R 486 TYR 0.023 0.002 TYR H 51 ARG 0.005 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6005 (p90) REVERT: R 377 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: R 423 TYR cc_start: 0.8065 (t80) cc_final: 0.7803 (t80) REVERT: R 441 LEU cc_start: 0.7122 (tt) cc_final: 0.6811 (mt) REVERT: H 25 GLU cc_start: 0.6963 (pm20) cc_final: 0.6441 (pm20) REVERT: H 72 TYR cc_start: 0.6912 (p90) cc_final: 0.6602 (p90) REVERT: L 28 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7188 (tt) REVERT: L 111 TYR cc_start: 0.8383 (m-80) cc_final: 0.7732 (m-80) outliers start: 23 outliers final: 15 residues processed: 117 average time/residue: 0.1562 time to fit residues: 22.2021 Evaluate side-chains 115 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 358 ILE Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 488 CYS Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 3458 Z= 0.254 Angle : 0.799 12.772 4695 Z= 0.400 Chirality : 0.048 0.183 499 Planarity : 0.007 0.139 604 Dihedral : 8.048 55.583 531 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.84 % Favored : 87.44 % Rotamer: Outliers : 5.54 % Allowed : 18.56 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.41), residues: 414 helix: -2.83 (1.15), residues: 12 sheet: -2.65 (0.41), residues: 133 loop : -1.89 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 59 HIS 0.004 0.002 HIS H 54 PHE 0.014 0.002 PHE L 95 TYR 0.020 0.001 TYR H 51 ARG 0.003 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 355 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7549 (ttp-170) REVERT: R 377 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: H 25 GLU cc_start: 0.6956 (pm20) cc_final: 0.6287 (pm20) REVERT: H 84 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8213 (ttmm) REVERT: H 134 TYR cc_start: 0.8354 (p90) cc_final: 0.7770 (p90) REVERT: L 28 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7199 (tt) REVERT: L 50 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7437 (tm-30) REVERT: L 62 GLN cc_start: 0.8741 (pt0) cc_final: 0.8429 (pt0) REVERT: L 74 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8387 (tt) REVERT: L 106 ASP cc_start: 0.6588 (m-30) cc_final: 0.6224 (m-30) REVERT: L 111 TYR cc_start: 0.8242 (m-80) cc_final: 0.7709 (m-80) outliers start: 20 outliers final: 13 residues processed: 121 average time/residue: 0.1820 time to fit residues: 25.9866 Evaluate side-chains 112 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 3458 Z= 0.241 Angle : 0.781 13.540 4695 Z= 0.383 Chirality : 0.047 0.161 499 Planarity : 0.007 0.133 604 Dihedral : 7.603 51.172 531 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % Rotamer: Outliers : 6.93 % Allowed : 21.05 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.99 (0.41), residues: 414 helix: -2.69 (1.21), residues: 12 sheet: -2.50 (0.41), residues: 132 loop : -1.70 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.023 0.002 PHE H 133 TYR 0.016 0.001 TYR H 51 ARG 0.004 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 355 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7563 (ttp-170) REVERT: R 377 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: H 25 GLU cc_start: 0.6924 (pm20) cc_final: 0.6254 (pm20) REVERT: H 134 TYR cc_start: 0.8482 (p90) cc_final: 0.7867 (p90) REVERT: L 59 TRP cc_start: 0.8792 (m100) cc_final: 0.8573 (m100) REVERT: L 62 GLN cc_start: 0.8666 (pt0) cc_final: 0.7993 (pt0) REVERT: L 74 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8286 (tt) REVERT: L 111 TYR cc_start: 0.8194 (m-80) cc_final: 0.7785 (m-80) outliers start: 25 outliers final: 17 residues processed: 111 average time/residue: 0.1846 time to fit residues: 24.5688 Evaluate side-chains 117 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3458 Z= 0.230 Angle : 0.741 13.609 4695 Z= 0.365 Chirality : 0.045 0.153 499 Planarity : 0.007 0.128 604 Dihedral : 7.012 50.134 529 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 6.65 % Allowed : 22.16 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.91 (0.41), residues: 414 helix: -3.18 (0.89), residues: 18 sheet: -2.37 (0.41), residues: 132 loop : -1.61 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.018 0.002 PHE H 133 TYR 0.024 0.002 TYR H 72 ARG 0.004 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7944 (t80) cc_final: 0.7637 (t80) REVERT: R 434 ILE cc_start: 0.9034 (mt) cc_final: 0.8611 (tt) REVERT: R 489 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5657 (t80) REVERT: H 25 GLU cc_start: 0.6902 (pm20) cc_final: 0.6167 (pm20) REVERT: H 71 ARG cc_start: 0.7332 (mtt90) cc_final: 0.7098 (mtt90) REVERT: H 72 TYR cc_start: 0.6934 (p90) cc_final: 0.6481 (p90) REVERT: H 123 TYR cc_start: 0.8575 (p90) cc_final: 0.8278 (p90) REVERT: L 25 GLN cc_start: 0.7138 (mt0) cc_final: 0.6820 (mt0) REVERT: L 59 TRP cc_start: 0.8738 (m100) cc_final: 0.8477 (m100) REVERT: L 62 GLN cc_start: 0.8596 (pt0) cc_final: 0.8091 (pt0) REVERT: L 73 TYR cc_start: 0.8939 (p90) cc_final: 0.8402 (p90) REVERT: L 74 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8307 (tt) REVERT: L 111 TYR cc_start: 0.8199 (m-80) cc_final: 0.7797 (m-80) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.1851 time to fit residues: 25.2286 Evaluate side-chains 119 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 3458 Z= 0.319 Angle : 0.771 14.028 4695 Z= 0.380 Chirality : 0.046 0.168 499 Planarity : 0.007 0.124 604 Dihedral : 6.714 47.726 527 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.84 % Favored : 87.68 % Rotamer: Outliers : 7.20 % Allowed : 22.44 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.91 (0.41), residues: 414 helix: -3.47 (0.75), residues: 18 sheet: -2.35 (0.41), residues: 131 loop : -1.60 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP R 353 HIS 0.002 0.001 HIS H 54 PHE 0.014 0.002 PHE H 133 TYR 0.018 0.001 TYR H 72 ARG 0.008 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7966 (t80) cc_final: 0.7587 (t80) REVERT: R 452 LEU cc_start: 0.8164 (mt) cc_final: 0.7962 (mm) REVERT: R 489 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5787 (t80) REVERT: H 25 GLU cc_start: 0.6984 (pm20) cc_final: 0.6273 (pm20) REVERT: H 72 TYR cc_start: 0.7093 (p90) cc_final: 0.6649 (p90) REVERT: H 123 TYR cc_start: 0.8571 (p90) cc_final: 0.8337 (p90) REVERT: L 25 GLN cc_start: 0.7448 (mt0) cc_final: 0.7055 (mt0) REVERT: L 62 GLN cc_start: 0.8632 (pt0) cc_final: 0.8193 (pt0) REVERT: L 73 TYR cc_start: 0.9000 (p90) cc_final: 0.8558 (p90) REVERT: L 74 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8482 (tt) REVERT: L 111 TYR cc_start: 0.8212 (m-80) cc_final: 0.7817 (m-80) outliers start: 26 outliers final: 23 residues processed: 111 average time/residue: 0.1589 time to fit residues: 21.2829 Evaluate side-chains 118 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3458 Z= 0.277 Angle : 0.774 13.965 4695 Z= 0.377 Chirality : 0.046 0.160 499 Planarity : 0.007 0.121 604 Dihedral : 6.594 47.148 527 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.11 % Favored : 88.41 % Rotamer: Outliers : 7.20 % Allowed : 23.82 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.76 (0.41), residues: 414 helix: -3.66 (0.68), residues: 18 sheet: -2.12 (0.44), residues: 123 loop : -1.59 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.017 0.002 PHE H 133 TYR 0.019 0.001 TYR H 72 ARG 0.006 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8002 (t80) cc_final: 0.7642 (t80) REVERT: R 452 LEU cc_start: 0.8160 (mt) cc_final: 0.7895 (mm) REVERT: R 489 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5787 (t80) REVERT: H 25 GLU cc_start: 0.7058 (pm20) cc_final: 0.6339 (pm20) REVERT: H 72 TYR cc_start: 0.7069 (p90) cc_final: 0.6661 (p90) REVERT: H 123 TYR cc_start: 0.8590 (p90) cc_final: 0.8320 (p90) REVERT: L 22 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8219 (p) REVERT: L 23 MET cc_start: 0.8189 (mmp) cc_final: 0.7979 (mmm) REVERT: L 62 GLN cc_start: 0.8640 (pt0) cc_final: 0.8173 (pt0) REVERT: L 73 TYR cc_start: 0.8969 (p90) cc_final: 0.8562 (p90) REVERT: L 74 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8508 (tt) REVERT: L 111 TYR cc_start: 0.8230 (m-80) cc_final: 0.7806 (m-80) outliers start: 26 outliers final: 21 residues processed: 112 average time/residue: 0.1549 time to fit residues: 20.9614 Evaluate side-chains 120 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3458 Z= 0.289 Angle : 0.762 14.002 4695 Z= 0.374 Chirality : 0.046 0.174 499 Planarity : 0.006 0.118 604 Dihedral : 6.634 47.394 527 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.08 % Favored : 87.44 % Rotamer: Outliers : 7.76 % Allowed : 23.27 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.76 (0.41), residues: 414 helix: -3.76 (0.69), residues: 18 sheet: -2.12 (0.44), residues: 123 loop : -1.57 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.016 0.002 PHE H 133 TYR 0.017 0.001 TYR H 72 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7987 (t80) cc_final: 0.7621 (t80) REVERT: R 452 LEU cc_start: 0.8125 (mt) cc_final: 0.7836 (mm) REVERT: R 489 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5960 (t80) REVERT: H 25 GLU cc_start: 0.7044 (pm20) cc_final: 0.6294 (pm20) REVERT: H 72 TYR cc_start: 0.7082 (p90) cc_final: 0.6679 (p90) REVERT: H 123 TYR cc_start: 0.8584 (p90) cc_final: 0.8301 (p90) REVERT: L 62 GLN cc_start: 0.8636 (pt0) cc_final: 0.8179 (pt0) REVERT: L 73 TYR cc_start: 0.8994 (p90) cc_final: 0.8538 (p90) REVERT: L 74 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8571 (tt) REVERT: L 111 TYR cc_start: 0.8191 (m-80) cc_final: 0.7781 (m-80) outliers start: 28 outliers final: 22 residues processed: 112 average time/residue: 0.1535 time to fit residues: 20.9051 Evaluate side-chains 116 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3458 Z= 0.256 Angle : 0.775 14.018 4695 Z= 0.378 Chirality : 0.046 0.151 499 Planarity : 0.006 0.116 604 Dihedral : 6.562 47.050 527 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.84 % Favored : 87.68 % Rotamer: Outliers : 6.37 % Allowed : 24.93 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.71 (0.41), residues: 414 helix: -3.78 (0.70), residues: 18 sheet: -2.08 (0.45), residues: 123 loop : -1.54 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.032 0.002 PHE H 133 TYR 0.017 0.001 TYR H 72 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7996 (t80) cc_final: 0.7643 (t80) REVERT: R 434 ILE cc_start: 0.9078 (mt) cc_final: 0.8608 (tt) REVERT: R 452 LEU cc_start: 0.8020 (mt) cc_final: 0.7734 (mm) REVERT: R 489 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5959 (t80) REVERT: H 25 GLU cc_start: 0.7026 (pm20) cc_final: 0.6257 (pm20) REVERT: H 72 TYR cc_start: 0.7040 (p90) cc_final: 0.6580 (p90) REVERT: L 62 GLN cc_start: 0.8614 (pt0) cc_final: 0.8160 (pt0) REVERT: L 73 TYR cc_start: 0.8984 (p90) cc_final: 0.8503 (p90) REVERT: L 74 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8591 (tt) REVERT: L 111 TYR cc_start: 0.8061 (m-80) cc_final: 0.7749 (m-80) outliers start: 23 outliers final: 20 residues processed: 107 average time/residue: 0.1495 time to fit residues: 19.5298 Evaluate side-chains 116 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3458 Z= 0.276 Angle : 0.775 13.938 4695 Z= 0.379 Chirality : 0.045 0.153 499 Planarity : 0.006 0.115 604 Dihedral : 6.522 46.879 527 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.32 % Favored : 87.20 % Rotamer: Outliers : 6.37 % Allowed : 24.93 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.71 (0.41), residues: 414 helix: -3.84 (0.71), residues: 18 sheet: -2.05 (0.45), residues: 123 loop : -1.56 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.024 0.002 PHE H 133 TYR 0.017 0.001 TYR H 72 ARG 0.006 0.001 ARG H 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7994 (t80) cc_final: 0.7620 (t80) REVERT: R 434 ILE cc_start: 0.9085 (mt) cc_final: 0.8613 (tt) REVERT: R 452 LEU cc_start: 0.8115 (mt) cc_final: 0.7816 (mm) REVERT: R 489 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5889 (t80) REVERT: H 25 GLU cc_start: 0.7039 (pm20) cc_final: 0.6291 (pm20) REVERT: H 72 TYR cc_start: 0.7085 (p90) cc_final: 0.6623 (p90) REVERT: L 62 GLN cc_start: 0.8642 (pt0) cc_final: 0.8146 (pt0) REVERT: L 73 TYR cc_start: 0.9010 (p90) cc_final: 0.8526 (p90) REVERT: L 74 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8589 (tt) REVERT: L 111 TYR cc_start: 0.8088 (m-80) cc_final: 0.7741 (m-80) outliers start: 23 outliers final: 20 residues processed: 106 average time/residue: 0.1489 time to fit residues: 19.2312 Evaluate side-chains 113 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.143248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119545 restraints weight = 5771.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123415 restraints weight = 3388.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126124 restraints weight = 2344.369| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3458 Z= 0.302 Angle : 0.780 13.852 4695 Z= 0.383 Chirality : 0.045 0.146 499 Planarity : 0.006 0.113 604 Dihedral : 6.552 47.104 527 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.56 % Favored : 86.96 % Rotamer: Outliers : 6.37 % Allowed : 24.93 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.74 (0.41), residues: 414 helix: -3.87 (0.70), residues: 18 sheet: -2.01 (0.46), residues: 123 loop : -1.60 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.022 0.002 PHE H 133 TYR 0.017 0.001 TYR H 72 ARG 0.006 0.001 ARG H 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.03 seconds wall clock time: 25 minutes 24.88 seconds (1524.88 seconds total)