Starting phenix.real_space_refine on Sun Mar 10 16:19:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr8_32718/03_2024/7wr8_32718.pdb" } resolution = 3.5 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= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2086 2.51 5 N 555 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 357": "NH1" <-> "NH2" Residue "R PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 442": "OD1" <-> "OD2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3286 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.50, per 1000 atoms: 0.76 Number of scatterers: 3286 At special positions: 0 Unit cell: (100.88, 62.4, 69.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 630 8.00 N 555 7.00 C 2086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 594.6 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 9.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.925A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.319A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.912A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.804A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.668A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.631A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.353A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.522A pdb=" N SER A 17 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 83 " --> pdb=" O SER A 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.146A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.857A pdb=" N THR B 73 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.891A pdb=" N THR B 103 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 45 " --> pdb=" O GLN B 36 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 174 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: 0.73 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 813 1.33 - 1.45: 759 1.45 - 1.57: 1783 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3373 Sorted by residual: bond pdb=" CG LEU R 441 " pdb=" CD2 LEU R 441 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" C GLU B 52 " pdb=" N ARG B 53 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.05e-02 9.07e+03 4.83e+00 bond pdb=" C ASP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" C SER B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 1.332 1.357 -0.026 1.34e-02 5.57e+03 3.63e+00 bond pdb=" CB TRP A 47 " pdb=" CG TRP A 47 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.30: 121 106.30 - 114.34: 1826 114.34 - 122.38: 2042 122.38 - 130.41: 591 130.41 - 138.45: 13 Bond angle restraints: 4593 Sorted by residual: angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 138.45 -22.15 3.50e+00 8.16e-02 4.00e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " ideal model delta sigma weight residual 116.20 120.25 -4.05 8.00e-01 1.56e+00 2.57e+01 angle pdb=" N ASN R 477 " pdb=" CA ASN R 477 " pdb=" C ASN R 477 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 121.31 118.05 3.26 7.40e-01 1.83e+00 1.94e+01 angle pdb=" C LYS B 49 " pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1763 15.93 - 31.86: 206 31.86 - 47.79: 45 47.79 - 63.72: 2 63.72 - 79.64: 4 Dihedral angle restraints: 2020 sinusoidal: 818 harmonic: 1202 Sorted by residual: dihedral pdb=" CA SER B 93 " pdb=" C SER B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " pdb=" CB CYS B 87 " ideal model delta sinusoidal sigma weight residual 93.00 47.57 45.43 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 2017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 342 0.052 - 0.105: 108 0.105 - 0.157: 42 0.157 - 0.210: 6 0.210 - 0.262: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" CB ILE A 19 " pdb=" CA ILE A 19 " pdb=" CG1 ILE A 19 " pdb=" CG2 ILE A 19 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.136 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG C 1 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 118 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 118 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP A 119 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 27 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO B 28 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 597 2.76 - 3.30: 2775 3.30 - 3.83: 5395 3.83 - 4.37: 6177 4.37 - 4.90: 11042 Nonbonded interactions: 25986 Sorted by model distance: nonbonded pdb=" NZ LYS R 440 " pdb=" N SER A 104 " model vdw 2.230 3.200 nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 29 " pdb=" OG SER B 29 " model vdw 2.302 2.440 nonbonded pdb=" NE2 HIS A 35 " pdb=" OD1 ASP A 99 " model vdw 2.307 2.520 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.328 2.440 ... (remaining 25981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 9.740 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.008 0.084 3373 Z= 0.558 Angle : 1.160 22.149 4593 Z= 0.630 Chirality : 0.062 0.262 502 Planarity : 0.010 0.111 591 Dihedral : 13.718 79.644 1245 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -3.48 (0.38), residues: 409 helix: -3.53 (0.89), residues: 21 sheet: -1.93 (0.42), residues: 139 loop : -2.50 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 47 HIS 0.004 0.001 HIS A 32 PHE 0.050 0.004 PHE R 456 TYR 0.035 0.003 TYR R 501 ARG 0.015 0.002 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.353 Fit side-chains REVERT: A 80 TYR cc_start: 0.7233 (m-80) cc_final: 0.7012 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1499 time to fit residues: 13.4413 Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3373 Z= 0.268 Angle : 0.688 10.426 4593 Z= 0.354 Chirality : 0.046 0.138 502 Planarity : 0.006 0.063 591 Dihedral : 6.627 27.228 524 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 1.42 % Allowed : 10.23 % Favored : 88.35 % 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: -3.25 (0.39), residues: 409 helix: -3.80 (0.60), residues: 33 sheet: -1.72 (0.42), residues: 144 loop : -2.21 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 47 HIS 0.002 0.001 HIS B 97 PHE 0.014 0.001 PHE A 101 TYR 0.018 0.002 TYR R 495 ARG 0.003 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.350 Fit side-chains REVERT: R 477 ASN cc_start: 0.7602 (t0) cc_final: 0.6871 (t0) REVERT: A 80 TYR cc_start: 0.7293 (m-10) cc_final: 0.6984 (m-80) outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1448 time to fit residues: 13.2124 Evaluate side-chains 71 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3373 Z= 0.283 Angle : 0.656 8.975 4593 Z= 0.335 Chirality : 0.046 0.136 502 Planarity : 0.005 0.048 591 Dihedral : 6.116 27.493 524 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 2.56 % Allowed : 11.36 % Favored : 86.08 % 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: -3.08 (0.40), residues: 409 helix: -4.21 (0.57), residues: 26 sheet: -1.59 (0.43), residues: 141 loop : -2.11 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 36 HIS 0.002 0.001 HIS R 505 PHE 0.014 0.001 PHE A 101 TYR 0.019 0.001 TYR R 495 ARG 0.004 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.367 Fit side-chains REVERT: R 396 TYR cc_start: 0.7842 (m-80) cc_final: 0.7576 (m-80) REVERT: B 91 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6834 (t0) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1455 time to fit residues: 13.8595 Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3373 Z= 0.228 Angle : 0.603 7.364 4593 Z= 0.308 Chirality : 0.045 0.131 502 Planarity : 0.005 0.052 591 Dihedral : 5.687 25.868 524 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.27 % Allowed : 13.35 % Favored : 84.38 % 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: -2.67 (0.42), residues: 409 helix: -4.05 (0.90), residues: 12 sheet: -1.56 (0.43), residues: 141 loop : -1.82 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.015 0.001 PHE R 456 TYR 0.016 0.001 TYR R 495 ARG 0.003 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.425 Fit side-chains REVERT: R 396 TYR cc_start: 0.7846 (m-80) cc_final: 0.7605 (m-80) REVERT: A 103 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.5019 (pp) REVERT: B 91 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7008 (t0) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.1595 time to fit residues: 14.2672 Evaluate side-chains 72 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0370 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3373 Z= 0.267 Angle : 0.649 13.450 4593 Z= 0.322 Chirality : 0.045 0.129 502 Planarity : 0.005 0.045 591 Dihedral : 5.635 27.014 524 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.41 % Allowed : 14.77 % Favored : 81.82 % 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: -2.86 (0.41), residues: 409 helix: -4.00 (0.68), residues: 20 sheet: -1.58 (0.43), residues: 141 loop : -1.94 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.013 0.001 PHE A 101 TYR 0.016 0.001 TYR R 495 ARG 0.004 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.393 Fit side-chains REVERT: R 396 TYR cc_start: 0.7828 (m-80) cc_final: 0.7596 (m-80) REVERT: A 80 TYR cc_start: 0.6861 (m-10) cc_final: 0.6490 (m-80) REVERT: A 103 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5135 (pp) REVERT: B 91 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7075 (t0) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.1593 time to fit residues: 13.4941 Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3373 Z= 0.292 Angle : 0.649 11.103 4593 Z= 0.328 Chirality : 0.045 0.125 502 Planarity : 0.005 0.050 591 Dihedral : 5.644 26.559 524 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.26 % Allowed : 14.20 % Favored : 81.53 % 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: -2.81 (0.41), residues: 409 helix: -4.02 (0.66), residues: 20 sheet: -1.49 (0.44), residues: 141 loop : -1.94 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP R 436 HIS 0.002 0.001 HIS R 505 PHE 0.017 0.002 PHE R 456 TYR 0.015 0.001 TYR R 495 ARG 0.004 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.353 Fit side-chains REVERT: R 374 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5520 (t80) REVERT: R 396 TYR cc_start: 0.7821 (m-80) cc_final: 0.7596 (m-80) REVERT: A 73 ASP cc_start: 0.6691 (m-30) cc_final: 0.5750 (m-30) REVERT: A 103 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5159 (pp) REVERT: A 109 TRP cc_start: 0.9014 (m-10) cc_final: 0.8703 (m-10) REVERT: B 91 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7008 (t0) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.1458 time to fit residues: 13.8948 Evaluate side-chains 82 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3373 Z= 0.299 Angle : 0.646 11.288 4593 Z= 0.328 Chirality : 0.045 0.128 502 Planarity : 0.005 0.079 591 Dihedral : 5.657 26.456 524 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.26 % Allowed : 16.19 % Favored : 79.55 % 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: -2.82 (0.41), residues: 409 helix: -4.03 (0.66), residues: 20 sheet: -1.43 (0.44), residues: 140 loop : -1.99 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 HIS 0.002 0.001 HIS R 505 PHE 0.017 0.002 PHE R 456 TYR 0.019 0.002 TYR A 80 ARG 0.005 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.355 Fit side-chains REVERT: R 374 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5552 (t80) REVERT: R 396 TYR cc_start: 0.7795 (m-80) cc_final: 0.7564 (m-80) REVERT: A 73 ASP cc_start: 0.6827 (m-30) cc_final: 0.5307 (m-30) REVERT: A 80 TYR cc_start: 0.6970 (m-10) cc_final: 0.6479 (m-80) REVERT: A 103 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.5142 (pp) REVERT: A 109 TRP cc_start: 0.9021 (m-10) cc_final: 0.8771 (m-10) REVERT: B 91 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7056 (t0) outliers start: 15 outliers final: 12 residues processed: 76 average time/residue: 0.1501 time to fit residues: 14.0324 Evaluate side-chains 79 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3373 Z= 0.236 Angle : 0.640 9.555 4593 Z= 0.326 Chirality : 0.046 0.236 502 Planarity : 0.005 0.078 591 Dihedral : 5.517 25.319 524 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 3.98 % Allowed : 17.90 % Favored : 78.12 % 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: -2.70 (0.41), residues: 409 helix: -3.97 (0.68), residues: 20 sheet: -1.40 (0.44), residues: 141 loop : -1.87 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.001 0.001 HIS A 35 PHE 0.020 0.001 PHE R 456 TYR 0.020 0.001 TYR A 80 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.306 Fit side-chains REVERT: R 396 TYR cc_start: 0.7802 (m-80) cc_final: 0.7547 (m-80) REVERT: A 73 ASP cc_start: 0.6867 (m-30) cc_final: 0.5091 (m-30) REVERT: A 80 TYR cc_start: 0.6891 (m-10) cc_final: 0.6432 (m-80) REVERT: A 103 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5063 (pp) REVERT: B 91 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7111 (t0) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.1432 time to fit residues: 13.3057 Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3373 Z= 0.246 Angle : 0.647 9.787 4593 Z= 0.328 Chirality : 0.046 0.239 502 Planarity : 0.005 0.062 591 Dihedral : 5.453 25.453 524 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.41 % Allowed : 19.03 % Favored : 77.56 % 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: -2.68 (0.41), residues: 409 helix: -3.98 (0.68), residues: 20 sheet: -1.39 (0.43), residues: 141 loop : -1.86 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 36 HIS 0.001 0.001 HIS A 35 PHE 0.020 0.001 PHE R 456 TYR 0.025 0.001 TYR A 80 ARG 0.004 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.382 Fit side-chains REVERT: A 73 ASP cc_start: 0.6655 (m-30) cc_final: 0.6418 (m-30) REVERT: A 103 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5000 (pp) REVERT: B 91 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7142 (t0) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.1407 time to fit residues: 12.7655 Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 0.0570 chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3373 Z= 0.186 Angle : 0.600 7.978 4593 Z= 0.307 Chirality : 0.045 0.191 502 Planarity : 0.005 0.070 591 Dihedral : 5.250 23.407 524 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.98 % Allowed : 19.32 % Favored : 76.70 % 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: -2.48 (0.41), residues: 409 helix: -3.92 (0.69), residues: 20 sheet: -0.93 (0.46), residues: 128 loop : -1.91 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.001 HIS A 35 PHE 0.022 0.002 PHE R 456 TYR 0.014 0.001 TYR A 80 ARG 0.004 0.001 ARG A 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.371 Fit side-chains REVERT: A 103 LEU cc_start: 0.5249 (OUTLIER) cc_final: 0.4894 (pp) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.1383 time to fit residues: 13.2608 Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0000 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 25 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.169855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138110 restraints weight = 3831.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141692 restraints weight = 2819.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144262 restraints weight = 2283.254| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3373 Z= 0.191 Angle : 0.598 8.876 4593 Z= 0.305 Chirality : 0.045 0.172 502 Planarity : 0.005 0.057 591 Dihedral : 5.119 23.532 524 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.69 % Allowed : 19.32 % Favored : 76.99 % 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: -2.54 (0.41), residues: 409 helix: -3.94 (0.68), residues: 20 sheet: -0.95 (0.46), residues: 131 loop : -1.98 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 119 HIS 0.001 0.000 HIS B 97 PHE 0.024 0.001 PHE R 456 TYR 0.012 0.001 TYR R 495 ARG 0.004 0.001 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.79 seconds wall clock time: 23 minutes 4.01 seconds (1384.01 seconds total)