Starting phenix.real_space_refine on Thu Jul 18 20:34:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jys_36730/07_2024/8jys_36730.cif" } resolution = 4.5 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= 0.005 sd= 0.042 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 2271 2.51 5 N 587 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 241 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain breaks: 1 Chain: "B" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 253 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 1 Chain: "D" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.79 Number of scatterers: 3522 At special positions: 0 Unit cell: (90.094, 67.36, 119.564, 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 648 8.00 N 587 7.00 C 2271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 596.9 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 11.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.391A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.104A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 383 through 388 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.808A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'D' and resid 356 through 358 removed outlier: 4.195A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.969A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 129 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: 0.75 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1112 1.34 - 1.47: 1024 1.47 - 1.59: 1473 1.59 - 1.72: 0 1.72 - 1.84: 16 Bond restraints: 3625 Sorted by residual: bond pdb=" N LEU C 109 " pdb=" CA LEU C 109 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.49e-02 4.50e+03 5.38e+00 bond pdb=" C GLU A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.26e-02 6.30e+03 3.84e+00 bond pdb=" C ALA D 520 " pdb=" N PRO D 521 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.33e-02 5.65e+03 3.07e+00 bond pdb=" C PRO B 373 " pdb=" O PRO B 373 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.30e-02 5.92e+03 1.81e+00 bond pdb=" C PRO D 521 " pdb=" O PRO D 521 " ideal model delta sigma weight residual 1.233 1.218 0.015 1.23e-02 6.61e+03 1.46e+00 ... (remaining 3620 not shown) Histogram of bond angle deviations from ideal: 102.29 - 108.66: 198 108.66 - 115.03: 1852 115.03 - 121.39: 1873 121.39 - 127.76: 979 127.76 - 134.13: 28 Bond angle restraints: 4930 Sorted by residual: angle pdb=" C ASN D 422 " pdb=" N TYR D 423 " pdb=" CA TYR D 423 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" CA TYR D 423 " pdb=" CB TYR D 423 " pdb=" CG TYR D 423 " ideal model delta sigma weight residual 113.90 120.74 -6.84 1.80e+00 3.09e-01 1.44e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 113.43 108.71 4.72 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CB LYS B 356 " pdb=" CG LYS B 356 " pdb=" CD LYS B 356 " ideal model delta sigma weight residual 111.30 119.15 -7.85 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C GLU B 465 " pdb=" CA GLU B 465 " pdb=" CB GLU B 465 " ideal model delta sigma weight residual 113.37 108.12 5.25 1.61e+00 3.86e-01 1.06e+01 ... (remaining 4925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 1704 16.01 - 32.01: 307 32.01 - 48.02: 81 48.02 - 64.02: 20 64.02 - 80.02: 6 Dihedral angle restraints: 2118 sinusoidal: 826 harmonic: 1292 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -21.65 -64.35 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 46.59 46.41 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CB CYS D 379 " pdb=" SG CYS D 379 " pdb=" SG CYS D 432 " pdb=" CB CYS D 432 " ideal model delta sinusoidal sigma weight residual 93.00 52.27 40.73 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 2115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 272 0.031 - 0.061: 132 0.061 - 0.092: 71 0.092 - 0.123: 30 0.123 - 0.153: 4 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA VAL D 511 " pdb=" N VAL D 511 " pdb=" C VAL D 511 " pdb=" CB VAL D 511 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 506 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 372 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO D 373 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 57 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 58 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 509 " -0.184 9.50e-02 1.11e+02 8.27e-02 4.24e+00 pdb=" NE ARG D 509 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 509 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 509 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 509 " -0.005 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 349 2.74 - 3.28: 3830 3.28 - 3.82: 5469 3.82 - 4.36: 6023 4.36 - 4.90: 9633 Nonbonded interactions: 25304 Sorted by model distance: nonbonded pdb=" O PHE D 347 " pdb=" OH TYR D 451 " model vdw 2.197 2.440 nonbonded pdb=" OG SER D 383 " pdb=" NZ LYS D 386 " model vdw 2.201 2.520 nonbonded pdb=" OG SER D 438 " pdb=" OD1 ASP D 442 " model vdw 2.217 2.440 nonbonded pdb=" NZ LYS D 478 " pdb=" O PRO D 479 " model vdw 2.244 2.520 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.245 2.440 ... (remaining 25299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 49 through 116) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 0.520 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.600 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.004 0.038 3625 Z= 0.257 Angle : 0.964 10.071 4930 Z= 0.516 Chirality : 0.048 0.153 509 Planarity : 0.008 0.083 644 Dihedral : 17.514 80.024 1272 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.12 % Rotamer: Outliers : 1.88 % Allowed : 38.34 % Favored : 59.79 % 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: -3.49 (0.38), residues: 425 helix: -2.42 (0.72), residues: 44 sheet: -0.81 (0.64), residues: 68 loop : -2.90 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.029 0.002 PHE B 456 TYR 0.022 0.002 TYR B 508 ARG 0.012 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 PHE cc_start: 0.7908 (t80) cc_final: 0.7666 (m-80) REVERT: B 451 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) REVERT: D 516 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tm-30) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.2281 time to fit residues: 27.7070 Evaluate side-chains 102 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.0670 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 422 ASN D 474 GLN D 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3625 Z= 0.198 Angle : 0.736 11.677 4930 Z= 0.368 Chirality : 0.045 0.160 509 Planarity : 0.006 0.052 644 Dihedral : 5.550 18.835 492 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.29 % Favored : 87.53 % Rotamer: Outliers : 0.80 % Allowed : 4.56 % Favored : 94.64 % 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: -3.18 (0.38), residues: 425 helix: -3.31 (0.54), residues: 46 sheet: -0.47 (0.63), residues: 64 loop : -2.49 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.006 0.002 HIS B 505 PHE 0.022 0.002 PHE B 490 TYR 0.021 0.002 TYR B 423 ARG 0.009 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 402 ILE cc_start: 0.9051 (tp) cc_final: 0.8817 (tp) REVERT: D 472 ILE cc_start: 0.8758 (tp) cc_final: 0.7644 (tp) REVERT: D 473 TYR cc_start: 0.8921 (t80) cc_final: 0.8370 (t80) REVERT: D 516 GLU cc_start: 0.8323 (tp30) cc_final: 0.7453 (tm-30) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.1976 time to fit residues: 29.3146 Evaluate side-chains 99 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3625 Z= 0.167 Angle : 0.683 10.653 4930 Z= 0.344 Chirality : 0.045 0.165 509 Planarity : 0.006 0.043 644 Dihedral : 5.377 18.216 492 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.00 % Favored : 87.06 % Rotamer: Outliers : 0.27 % Allowed : 4.29 % Favored : 95.44 % 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: -3.02 (0.39), residues: 425 helix: -2.94 (0.56), residues: 52 sheet: -0.45 (0.60), residues: 69 loop : -2.39 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.019 0.002 PHE D 400 TYR 0.020 0.001 TYR D 495 ARG 0.006 0.001 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 394 ASN cc_start: 0.8991 (t0) cc_final: 0.8224 (p0) REVERT: D 402 ILE cc_start: 0.9096 (tp) cc_final: 0.8770 (tp) REVERT: D 425 LEU cc_start: 0.9071 (pp) cc_final: 0.8821 (pp) REVERT: D 473 TYR cc_start: 0.8929 (t80) cc_final: 0.8485 (t80) REVERT: D 486 PHE cc_start: 0.7445 (t80) cc_final: 0.7030 (t80) REVERT: D 516 GLU cc_start: 0.7951 (tp30) cc_final: 0.6887 (tm-30) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2116 time to fit residues: 31.2673 Evaluate side-chains 97 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3625 Z= 0.345 Angle : 0.809 11.174 4930 Z= 0.417 Chirality : 0.048 0.170 509 Planarity : 0.006 0.041 644 Dihedral : 6.163 21.779 492 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.94 % Allowed : 15.29 % Favored : 83.76 % Rotamer: Outliers : 0.54 % Allowed : 5.36 % Favored : 94.10 % 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: -3.06 (0.39), residues: 425 helix: -2.55 (0.69), residues: 46 sheet: -0.65 (0.61), residues: 66 loop : -2.47 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 53 HIS 0.003 0.001 HIS B 519 PHE 0.021 0.003 PHE B 347 TYR 0.028 0.003 TYR B 453 ARG 0.008 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 453 TYR cc_start: 0.8685 (t80) cc_final: 0.7730 (t80) REVERT: B 465 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: B 471 GLU cc_start: 0.9005 (tp30) cc_final: 0.8802 (tp30) REVERT: B 489 TYR cc_start: 0.7884 (m-80) cc_final: 0.7570 (m-80) REVERT: B 517 LEU cc_start: 0.8910 (mp) cc_final: 0.8634 (tt) REVERT: C 106 TYR cc_start: 0.6356 (p90) cc_final: 0.6133 (p90) REVERT: D 396 TYR cc_start: 0.8629 (m-80) cc_final: 0.8368 (m-80) REVERT: D 402 ILE cc_start: 0.9086 (tp) cc_final: 0.8873 (tp) REVERT: D 473 TYR cc_start: 0.9133 (t80) cc_final: 0.8748 (t80) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.2015 time to fit residues: 27.8219 Evaluate side-chains 89 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3625 Z= 0.241 Angle : 0.718 10.819 4930 Z= 0.365 Chirality : 0.046 0.190 509 Planarity : 0.005 0.041 644 Dihedral : 5.780 20.536 492 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.41 % Favored : 85.41 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -3.21 (0.39), residues: 425 helix: -2.83 (0.67), residues: 46 sheet: -0.78 (0.61), residues: 63 loop : -2.52 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.002 0.001 HIS D 519 PHE 0.021 0.002 PHE D 400 TYR 0.017 0.002 TYR D 421 ARG 0.007 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8343 (m-80) cc_final: 0.7831 (m-10) REVERT: B 453 TYR cc_start: 0.8342 (t80) cc_final: 0.7974 (t80) REVERT: B 468 ILE cc_start: 0.9153 (tt) cc_final: 0.8905 (tt) REVERT: B 471 GLU cc_start: 0.8986 (tp30) cc_final: 0.8762 (tp30) REVERT: B 489 TYR cc_start: 0.7756 (m-80) cc_final: 0.7429 (m-80) REVERT: B 493 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8357 (tpp80) REVERT: D 396 TYR cc_start: 0.8645 (m-80) cc_final: 0.8378 (m-80) REVERT: D 402 ILE cc_start: 0.9022 (tp) cc_final: 0.8739 (tp) REVERT: D 425 LEU cc_start: 0.9119 (pp) cc_final: 0.8917 (pp) REVERT: D 473 TYR cc_start: 0.9059 (t80) cc_final: 0.8656 (t80) REVERT: D 516 GLU cc_start: 0.8265 (tp30) cc_final: 0.7628 (tm-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1915 time to fit residues: 27.7647 Evaluate side-chains 90 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.0270 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3625 Z= 0.219 Angle : 0.743 12.018 4930 Z= 0.370 Chirality : 0.047 0.284 509 Planarity : 0.006 0.052 644 Dihedral : 5.724 19.625 492 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.41 % Favored : 85.41 % Rotamer: Outliers : 0.27 % Allowed : 2.41 % Favored : 97.32 % 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: -3.02 (0.39), residues: 425 helix: -2.69 (0.77), residues: 41 sheet: -0.69 (0.60), residues: 69 loop : -2.41 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.023 0.002 PHE B 375 TYR 0.022 0.002 TYR B 508 ARG 0.006 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8394 (m-80) cc_final: 0.7866 (m-80) REVERT: B 468 ILE cc_start: 0.9130 (tt) cc_final: 0.8907 (tt) REVERT: B 471 GLU cc_start: 0.8999 (tp30) cc_final: 0.8742 (tp30) REVERT: B 489 TYR cc_start: 0.7642 (m-80) cc_final: 0.7421 (m-80) REVERT: C 100 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6207 (pp30) REVERT: D 402 ILE cc_start: 0.9037 (tp) cc_final: 0.8731 (tp) REVERT: D 425 LEU cc_start: 0.9079 (pp) cc_final: 0.8841 (pp) REVERT: D 473 TYR cc_start: 0.8975 (t80) cc_final: 0.8607 (t80) REVERT: D 492 LEU cc_start: 0.9166 (mm) cc_final: 0.8930 (mp) REVERT: D 516 GLU cc_start: 0.8207 (tp30) cc_final: 0.7908 (tp30) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1803 time to fit residues: 25.9451 Evaluate side-chains 89 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3625 Z= 0.207 Angle : 0.716 11.756 4930 Z= 0.363 Chirality : 0.046 0.206 509 Planarity : 0.005 0.046 644 Dihedral : 5.599 19.488 492 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -3.03 (0.39), residues: 425 helix: -2.77 (0.70), residues: 40 sheet: -0.61 (0.61), residues: 68 loop : -2.44 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.018 0.002 PHE D 400 TYR 0.018 0.002 TYR D 421 ARG 0.006 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7649 (mpt180) cc_final: 0.7289 (mpt180) REVERT: B 453 TYR cc_start: 0.8276 (t80) cc_final: 0.7719 (t80) REVERT: B 489 TYR cc_start: 0.7687 (m-80) cc_final: 0.7406 (m-80) REVERT: D 402 ILE cc_start: 0.8981 (tp) cc_final: 0.8698 (tp) REVERT: D 473 TYR cc_start: 0.8947 (t80) cc_final: 0.8530 (t80) REVERT: D 506 GLN cc_start: 0.8601 (mt0) cc_final: 0.8395 (mt0) REVERT: D 516 GLU cc_start: 0.8193 (tp30) cc_final: 0.7850 (tp30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1873 time to fit residues: 24.9735 Evaluate side-chains 86 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3625 Z= 0.344 Angle : 0.800 12.071 4930 Z= 0.413 Chirality : 0.049 0.202 509 Planarity : 0.006 0.068 644 Dihedral : 6.352 24.007 492 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 1.18 % Allowed : 17.18 % Favored : 81.65 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.39), residues: 425 helix: -2.87 (0.67), residues: 46 sheet: -0.86 (0.60), residues: 64 loop : -2.50 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 436 HIS 0.003 0.001 HIS D 505 PHE 0.032 0.002 PHE B 375 TYR 0.024 0.002 TYR B 421 ARG 0.011 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7613 (mpt180) cc_final: 0.6927 (mpt180) REVERT: D 402 ILE cc_start: 0.8991 (tp) cc_final: 0.8749 (tp) REVERT: D 473 TYR cc_start: 0.8981 (t80) cc_final: 0.8507 (t80) REVERT: D 506 GLN cc_start: 0.8739 (mt0) cc_final: 0.8506 (mt0) REVERT: D 516 GLU cc_start: 0.8239 (tp30) cc_final: 0.7851 (tm-30) REVERT: D 518 LEU cc_start: 0.8966 (tp) cc_final: 0.8723 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1973 time to fit residues: 24.8790 Evaluate side-chains 78 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3625 Z= 0.218 Angle : 0.733 11.779 4930 Z= 0.370 Chirality : 0.047 0.230 509 Planarity : 0.005 0.047 644 Dihedral : 5.981 22.620 492 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.47 % Favored : 86.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.39), residues: 425 helix: -3.11 (0.64), residues: 40 sheet: -0.81 (0.59), residues: 68 loop : -2.49 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.017 0.002 PHE D 400 TYR 0.019 0.002 TYR B 423 ARG 0.008 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7268 (mpp-170) cc_final: 0.6989 (mtm-85) REVERT: B 489 TYR cc_start: 0.7773 (m-80) cc_final: 0.7431 (m-80) REVERT: D 402 ILE cc_start: 0.8939 (tp) cc_final: 0.8665 (tp) REVERT: D 420 ASP cc_start: 0.8464 (p0) cc_final: 0.8257 (p0) REVERT: D 473 TYR cc_start: 0.8870 (t80) cc_final: 0.8385 (t80) REVERT: D 492 LEU cc_start: 0.9223 (mm) cc_final: 0.9013 (mp) REVERT: D 516 GLU cc_start: 0.8170 (tp30) cc_final: 0.7851 (tp30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1848 time to fit residues: 24.4404 Evaluate side-chains 90 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3625 Z= 0.175 Angle : 0.720 11.743 4930 Z= 0.358 Chirality : 0.046 0.222 509 Planarity : 0.005 0.050 644 Dihedral : 5.652 20.149 492 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.88 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.14 (0.39), residues: 425 helix: -3.07 (0.73), residues: 34 sheet: -0.85 (0.58), residues: 70 loop : -2.47 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE D 400 TYR 0.016 0.001 TYR D 351 ARG 0.007 0.001 ARG B 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8634 (pm20) cc_final: 0.7281 (tp30) REVERT: B 354 ASN cc_start: 0.9207 (t0) cc_final: 0.8904 (t0) REVERT: B 356 LYS cc_start: 0.9178 (tppt) cc_final: 0.8716 (tppt) REVERT: B 453 TYR cc_start: 0.7913 (t80) cc_final: 0.7619 (t80) REVERT: B 489 TYR cc_start: 0.7672 (m-80) cc_final: 0.7471 (m-80) REVERT: B 493 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8049 (tpp80) REVERT: D 402 ILE cc_start: 0.8901 (tp) cc_final: 0.8573 (tp) REVERT: D 473 TYR cc_start: 0.8733 (t80) cc_final: 0.8224 (t80) REVERT: D 516 GLU cc_start: 0.8148 (tp30) cc_final: 0.7830 (tp30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1971 time to fit residues: 27.6672 Evaluate side-chains 90 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091091 restraints weight = 13069.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093858 restraints weight = 8222.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095894 restraints weight = 5820.615| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3625 Z= 0.211 Angle : 0.724 11.397 4930 Z= 0.363 Chirality : 0.047 0.231 509 Planarity : 0.005 0.045 644 Dihedral : 5.670 20.003 492 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.88 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -3.10 (0.39), residues: 425 helix: -3.00 (0.75), residues: 34 sheet: -0.84 (0.58), residues: 70 loop : -2.44 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 436 HIS 0.001 0.001 HIS B 519 PHE 0.015 0.002 PHE D 400 TYR 0.018 0.001 TYR D 495 ARG 0.007 0.001 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1257.22 seconds wall clock time: 23 minutes 7.86 seconds (1387.86 seconds total)