Starting phenix.real_space_refine on Fri Apr 5 15:17:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm0_32596/04_2024/7wm0_32596.pdb" } resolution = 3.35 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= 0.005 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 17 5.16 5 C 2146 2.51 5 N 573 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3376 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1554 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.82 Number of scatterers: 3376 At special positions: 0 Unit cell: (71.994, 79.092, 70.98, 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 17 16.00 O 640 8.00 N 573 7.00 C 2146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 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 NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 980.4 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.4% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.113A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 243 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: 0.94 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1016 1.34 - 1.46: 795 1.46 - 1.59: 1630 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3463 Sorted by residual: bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL L 88 " pdb=" CA VAL L 88 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N LYS B 444 " pdb=" CA LYS B 444 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ASN H 54 " pdb=" CA ASN H 54 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.66e+00 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.55: 121 106.55 - 113.50: 1774 113.50 - 120.44: 1459 120.44 - 127.39: 1326 127.39 - 134.33: 27 Bond angle restraints: 4707 Sorted by residual: angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.71 105.91 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 109.85 116.70 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 112.90 108.75 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" C VAL B 407 " pdb=" N ARG B 408 " pdb=" CA ARG B 408 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N TYR B 369 " pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 112.89 108.02 4.87 1.24e+00 6.50e-01 1.54e+01 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1807 13.97 - 27.95: 173 27.95 - 41.92: 53 41.92 - 55.90: 11 55.90 - 69.87: 7 Dihedral angle restraints: 2051 sinusoidal: 810 harmonic: 1241 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" C ARG B 466 " pdb=" N ARG B 466 " pdb=" CA ARG B 466 " pdb=" CB ARG B 466 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C TYR B 365 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " pdb=" CB TYR B 365 " ideal model delta harmonic sigma weight residual -122.60 -114.17 -8.43 0 2.50e+00 1.60e-01 1.14e+01 ... (remaining 2048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 340 0.067 - 0.133: 117 0.133 - 0.200: 39 0.200 - 0.267: 8 0.267 - 0.333: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG B 466 " pdb=" N ARG B 466 " pdb=" C ARG B 466 " pdb=" CB ARG B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA TYR H 115 " pdb=" N TYR H 115 " pdb=" C TYR H 115 " pdb=" CB TYR H 115 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 503 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.355 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG B1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 353 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C TRP B 353 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 353 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 354 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 116 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C GLY H 116 " 0.037 2.00e-02 2.50e+03 pdb=" O GLY H 116 " -0.014 2.00e-02 2.50e+03 pdb=" N MET H 117 " -0.013 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 1446 2.90 - 3.40: 3021 3.40 - 3.90: 5401 3.90 - 4.40: 6057 4.40 - 4.90: 10403 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASP H 62 " pdb=" N SER H 63 " model vdw 2.405 2.520 nonbonded pdb=" OD1 ASP H 118 " pdb=" N VAL H 119 " model vdw 2.423 2.520 nonbonded pdb=" NH1 ARG L 59 " pdb=" O PHE L 67 " model vdw 2.452 2.520 nonbonded pdb=" O SER H 130 " pdb=" OG SER H 130 " model vdw 2.456 2.440 nonbonded pdb=" NE2 GLN L 95 " pdb=" O PRO L 100 " model vdw 2.457 2.520 ... (remaining 26323 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 11.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 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 : 0.009 0.044 3463 Z= 0.597 Angle : 1.223 8.086 4707 Z= 0.850 Chirality : 0.078 0.333 506 Planarity : 0.013 0.304 611 Dihedral : 12.602 69.871 1247 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.87 (0.38), residues: 424 helix: -4.69 (0.22), residues: 39 sheet: -1.16 (0.45), residues: 142 loop : -1.89 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.002 PHE B 515 TYR 0.012 0.002 TYR B 396 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8174 (m-30) cc_final: 0.7972 (m-30) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1642 time to fit residues: 16.8096 Evaluate side-chains 55 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3463 Z= 0.278 Angle : 0.705 6.852 4707 Z= 0.369 Chirality : 0.047 0.181 506 Planarity : 0.005 0.036 611 Dihedral : 6.476 55.686 499 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.03 % Allowed : 11.85 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.39), residues: 424 helix: -4.55 (0.42), residues: 20 sheet: -0.60 (0.46), residues: 137 loop : -1.32 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.007 0.002 HIS H 35 PHE 0.024 0.002 PHE B 464 TYR 0.015 0.002 TYR L 92 ARG 0.005 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.7083 (mtm) cc_final: 0.6486 (mtm) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1607 time to fit residues: 15.3582 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3463 Z= 0.205 Angle : 0.618 7.478 4707 Z= 0.319 Chirality : 0.043 0.157 506 Planarity : 0.004 0.030 611 Dihedral : 6.057 57.151 499 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.68 % Allowed : 14.33 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.40), residues: 424 helix: -4.33 (0.65), residues: 20 sheet: -0.07 (0.47), residues: 131 loop : -1.05 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.006 0.002 HIS H 35 PHE 0.009 0.001 PHE B 464 TYR 0.014 0.002 TYR B 473 ARG 0.003 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.7014 (mtm) cc_final: 0.6649 (mtm) REVERT: L 50 GLN cc_start: 0.7488 (mp10) cc_final: 0.7086 (mp10) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.1365 time to fit residues: 12.8433 Evaluate side-chains 68 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 3463 Z= 0.368 Angle : 0.795 9.780 4707 Z= 0.416 Chirality : 0.047 0.162 506 Planarity : 0.006 0.039 611 Dihedral : 7.288 58.730 499 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.79 % Allowed : 17.36 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.40), residues: 424 helix: -4.76 (0.41), residues: 26 sheet: 0.19 (0.50), residues: 122 loop : -1.18 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 436 HIS 0.005 0.002 HIS H 35 PHE 0.013 0.003 PHE B 377 TYR 0.051 0.003 TYR B 508 ARG 0.007 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.383 Fit side-chains REVERT: B 449 TYR cc_start: 0.6833 (t80) cc_final: 0.6460 (t80) REVERT: H 102 MET cc_start: 0.7068 (mtm) cc_final: 0.6825 (mtm) REVERT: L 55 LEU cc_start: 0.7615 (mt) cc_final: 0.7353 (mt) outliers start: 21 outliers final: 18 residues processed: 84 average time/residue: 0.1445 time to fit residues: 15.2671 Evaluate side-chains 77 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.0040 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3463 Z= 0.247 Angle : 0.688 9.429 4707 Z= 0.352 Chirality : 0.044 0.146 506 Planarity : 0.004 0.034 611 Dihedral : 6.693 54.850 499 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.79 % Allowed : 22.04 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 424 helix: -4.86 (0.36), residues: 26 sheet: 0.16 (0.49), residues: 132 loop : -1.27 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.002 PHE B 429 TYR 0.044 0.002 TYR B 508 ARG 0.005 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 449 TYR cc_start: 0.6527 (t80) cc_final: 0.6167 (t80) outliers start: 21 outliers final: 19 residues processed: 79 average time/residue: 0.1247 time to fit residues: 12.6031 Evaluate side-chains 78 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3463 Z= 0.222 Angle : 0.670 9.237 4707 Z= 0.341 Chirality : 0.043 0.160 506 Planarity : 0.004 0.032 611 Dihedral : 6.438 52.451 499 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.61 % Allowed : 24.52 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.40), residues: 424 helix: -4.88 (0.36), residues: 26 sheet: 0.19 (0.48), residues: 129 loop : -1.34 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE B 374 TYR 0.043 0.002 TYR B 508 ARG 0.003 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.6711 (mtm) cc_final: 0.6454 (mtm) REVERT: L 76 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: L 84 GLU cc_start: 0.4580 (mp0) cc_final: 0.3041 (pt0) outliers start: 24 outliers final: 21 residues processed: 77 average time/residue: 0.1394 time to fit residues: 13.4467 Evaluate side-chains 81 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3463 Z= 0.338 Angle : 0.762 9.215 4707 Z= 0.397 Chirality : 0.047 0.164 506 Planarity : 0.005 0.038 611 Dihedral : 6.948 49.794 499 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 7.71 % Allowed : 24.79 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.40), residues: 424 helix: -4.98 (0.28), residues: 26 sheet: -0.04 (0.47), residues: 130 loop : -1.50 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 436 HIS 0.004 0.002 HIS B 505 PHE 0.016 0.002 PHE B 374 TYR 0.049 0.003 TYR B 508 ARG 0.003 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 0.404 Fit side-chains REVERT: L 47 GLN cc_start: 0.5738 (tm-30) cc_final: 0.5434 (tm-30) outliers start: 28 outliers final: 23 residues processed: 82 average time/residue: 0.1257 time to fit residues: 13.3080 Evaluate side-chains 84 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.7698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3463 Z= 0.201 Angle : 0.654 7.014 4707 Z= 0.338 Chirality : 0.044 0.151 506 Planarity : 0.004 0.038 611 Dihedral : 6.297 46.301 499 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.34 % Allowed : 27.00 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.39), residues: 424 helix: -4.96 (0.29), residues: 26 sheet: -0.05 (0.47), residues: 131 loop : -1.46 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 436 HIS 0.003 0.001 HIS B 505 PHE 0.008 0.001 PHE B 374 TYR 0.038 0.002 TYR B 508 ARG 0.003 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.338 Fit side-chains REVERT: H 102 MET cc_start: 0.6910 (mtm) cc_final: 0.6049 (mtm) outliers start: 23 outliers final: 20 residues processed: 81 average time/residue: 0.1348 time to fit residues: 13.8250 Evaluate side-chains 79 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 75 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.8038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3463 Z= 0.291 Angle : 0.748 10.286 4707 Z= 0.383 Chirality : 0.046 0.157 506 Planarity : 0.005 0.045 611 Dihedral : 6.790 49.207 499 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.61 % Allowed : 26.17 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.39), residues: 424 helix: -5.00 (0.25), residues: 26 sheet: -0.05 (0.48), residues: 130 loop : -1.63 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 436 HIS 0.006 0.001 HIS B 505 PHE 0.014 0.002 PHE B 374 TYR 0.047 0.003 TYR B 508 ARG 0.006 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.376 Fit side-chains REVERT: B 449 TYR cc_start: 0.6782 (t80) cc_final: 0.6424 (t80) outliers start: 24 outliers final: 20 residues processed: 80 average time/residue: 0.1257 time to fit residues: 12.9123 Evaluate side-chains 81 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3463 Z= 0.191 Angle : 0.683 7.639 4707 Z= 0.350 Chirality : 0.044 0.143 506 Planarity : 0.004 0.042 611 Dihedral : 6.203 46.614 499 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.96 % Allowed : 28.10 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 424 helix: -4.97 (0.26), residues: 26 sheet: -0.21 (0.47), residues: 131 loop : -1.53 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.003 0.001 HIS B 505 PHE 0.008 0.001 PHE B 374 TYR 0.044 0.002 TYR B 508 ARG 0.007 0.001 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.383 Fit side-chains REVERT: B 449 TYR cc_start: 0.6509 (t80) cc_final: 0.6249 (t80) REVERT: H 102 MET cc_start: 0.6728 (mtm) cc_final: 0.6052 (mtm) outliers start: 18 outliers final: 17 residues processed: 75 average time/residue: 0.1124 time to fit residues: 11.0699 Evaluate side-chains 76 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN ** L 27 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 = 0.4332 r_free = 0.4332 target = 0.153773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.141332 restraints weight = 7427.039| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.96 r_work: 0.4007 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.8201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3463 Z= 0.265 Angle : 0.724 8.463 4707 Z= 0.372 Chirality : 0.045 0.146 506 Planarity : 0.005 0.046 611 Dihedral : 6.538 49.500 499 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.61 % Allowed : 26.72 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.39), residues: 424 helix: -4.96 (0.25), residues: 26 sheet: -0.26 (0.47), residues: 130 loop : -1.54 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE B 374 TYR 0.048 0.002 TYR B 508 ARG 0.007 0.001 ARG B 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.82 seconds wall clock time: 26 minutes 44.03 seconds (1604.03 seconds total)