Starting phenix.real_space_refine on Tue Feb 13 12:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/02_2024/8ero_28556_updated.pdb" } resolution = 3.2 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= 0.006 sd= 0.191 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 50 5.16 5 C 4156 2.51 5 N 892 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6154 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "B" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-2': 11, 'LBN:plan-3': 12, 'LBN:plan-1': 11} Unresolved non-hydrogen planarities: 116 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-2': 11, 'LBN:plan-3': 12, 'LBN:plan-1': 11} Unresolved non-hydrogen planarities: 116 Time building chain proxies: 4.01, per 1000 atoms: 0.65 Number of scatterers: 6154 At special positions: 0 Unit cell: (78.1, 122.1, 70.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 4 11.99 O 1044 8.00 N 892 7.00 C 4156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 71.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 41 through 56 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 63 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 94 through 119 Processing helix chain 'A' and resid 126 through 151 removed outlier: 3.550A pdb=" N MET A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 180 Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.953A pdb=" N TRP A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 294 through 317 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 349 through 377 Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 41 through 56 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 63 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 94 through 119 Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.550A pdb=" N MET B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 161 through 180 Processing helix chain 'B' and resid 191 through 208 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.953A pdb=" N TRP B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 248 Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 294 through 317 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 377 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.825A pdb=" N LEU A 184 " --> pdb=" O SER A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.825A pdb=" N LEU B 184 " --> pdb=" O SER B 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 378 hydrogen bonds defined for protein. 954 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: 1.45 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 892 1.32 - 1.44: 1631 1.44 - 1.56: 3663 1.56 - 1.69: 14 1.69 - 1.81: 74 Bond restraints: 6274 Sorted by residual: bond pdb=" C3' CDP A 513 " pdb=" C4' CDP A 513 " ideal model delta sigma weight residual 1.305 1.521 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C3' CDP B 516 " pdb=" C4' CDP B 516 " ideal model delta sigma weight residual 1.305 1.521 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C4' CDP A 513 " pdb=" O4' CDP A 513 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C4' CDP B 516 " pdb=" O4' CDP B 516 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" O2 LBN B 515 " pdb=" P1 LBN B 515 " ideal model delta sigma weight residual 1.650 1.482 0.168 2.00e-02 2.50e+03 7.07e+01 ... (remaining 6269 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.91: 154 105.91 - 112.93: 3303 112.93 - 119.94: 2294 119.94 - 126.95: 2584 126.95 - 133.97: 81 Bond angle restraints: 8416 Sorted by residual: angle pdb=" O1 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O2 LBN B 515 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O1 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O2 LBN A 512 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O3 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O4 LBN A 512 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O4 LBN B 515 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O1 LBN B 507 " pdb=" P1 LBN B 507 " pdb=" O2 LBN B 507 " ideal model delta sigma weight residual 93.45 104.29 -10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 8411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.56: 3544 31.56 - 63.12: 142 63.12 - 94.68: 14 94.68 - 126.24: 24 126.24 - 157.80: 4 Dihedral angle restraints: 3728 sinusoidal: 1626 harmonic: 2102 Sorted by residual: dihedral pdb=" O5 LBN B 515 " pdb=" C2 LBN B 515 " pdb=" C3 LBN B 515 " pdb=" O7 LBN B 515 " ideal model delta sinusoidal sigma weight residual 62.67 -139.53 -157.80 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O5 LBN A 512 " pdb=" C2 LBN A 512 " pdb=" C3 LBN A 512 " pdb=" O7 LBN A 512 " ideal model delta sinusoidal sigma weight residual 62.67 -139.53 -157.80 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C32 LBN A 509 " pdb=" C33 LBN A 509 " pdb=" C4 LBN A 509 " pdb=" C7 LBN A 509 " ideal model delta sinusoidal sigma weight residual 179.89 -48.49 -131.62 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 3725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 738 0.049 - 0.098: 176 0.098 - 0.147: 32 0.147 - 0.196: 0 0.196 - 0.246: 4 Chirality restraints: 950 Sorted by residual: chirality pdb=" C3' CDP A 513 " pdb=" C2' CDP A 513 " pdb=" C4' CDP A 513 " pdb=" O3' CDP A 513 " both_signs ideal model delta sigma weight residual False -2.39 -2.64 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3' CDP B 516 " pdb=" C2' CDP B 516 " pdb=" C4' CDP B 516 " pdb=" O3' CDP B 516 " both_signs ideal model delta sigma weight residual False -2.39 -2.64 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 LBN A 504 " pdb=" C1 LBN A 504 " pdb=" C3 LBN A 504 " pdb=" O7 LBN A 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 947 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 507 " -0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN B 507 " 0.234 2.00e-02 2.50e+03 pdb=" C5 LBN B 507 " 0.225 2.00e-02 2.50e+03 pdb=" C8 LBN B 507 " -0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 504 " 0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN A 504 " -0.234 2.00e-02 2.50e+03 pdb=" C5 LBN A 504 " -0.225 2.00e-02 2.50e+03 pdb=" C8 LBN A 504 " 0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C TYR A 238 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 50 2.59 - 3.17: 5235 3.17 - 3.74: 8782 3.74 - 4.32: 11684 4.32 - 4.90: 20344 Nonbonded interactions: 46095 Sorted by model distance: nonbonded pdb=" OD1 ASP A 132 " pdb="MG MG A 501 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASP B 132 " pdb="MG MG B 504 " model vdw 2.011 2.170 nonbonded pdb="MG MG B 505 " pdb=" O1A CDP B 516 " model vdw 2.024 2.170 nonbonded pdb="MG MG A 502 " pdb=" O1A CDP A 513 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A 136 " pdb="MG MG A 501 " model vdw 2.060 2.170 ... (remaining 46090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 383 or resid 503 or (resid 506 and (name C10 or \ name C13 or name C16 or name C29 or name C30 or name C31 or name C32 or name C3 \ 3 or name C4 or name C7 )) or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 509 or (re \ sid 510 and (name C10 or name C13 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) or re \ sid 511 or (resid 512 and (name C25 or name C26 or name C27 or name C28 or name \ C29 or name C30 or name C31 or name C32)) or resid 514 or (resid 515 and (name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or na \ me C32)))) selection = (chain 'B' and (resid 20 through 383 or (resid 503 and (name C10 or name C13 or \ name C16 or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 \ or name C7 )) or resid 506 or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 511 or (re \ sid 512 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32)) or (resid 514 and (name C10 or name C13 or name C26 \ or name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name \ C33 or name C4 or name C7 )) or (resid 515 and (name C25 or name C26 or name C27 \ or name C28 or name C29 or name C30 or name C31 or name C32)))) } 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: 0.370 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: 1.990 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.400 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.010 0.216 6274 Z= 0.509 Angle : 0.855 15.587 8416 Z= 0.402 Chirality : 0.044 0.246 950 Planarity : 0.012 0.229 972 Dihedral : 20.298 157.797 2384 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.32), residues: 724 helix: 1.78 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 176 HIS 0.006 0.001 HIS B 376 PHE 0.015 0.002 PHE A 165 TYR 0.011 0.001 TYR A 282 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.650 Fit side-chains REVERT: A 60 TRP cc_start: 0.8512 (p-90) cc_final: 0.8231 (p-90) REVERT: A 159 TRP cc_start: 0.8535 (m100) cc_final: 0.8180 (m100) REVERT: A 193 GLU cc_start: 0.7346 (mp0) cc_final: 0.6891 (mp0) REVERT: A 201 MET cc_start: 0.6745 (ttp) cc_final: 0.6442 (ttp) REVERT: A 262 THR cc_start: 0.7762 (t) cc_final: 0.7363 (p) REVERT: A 292 GLN cc_start: 0.7658 (tt0) cc_final: 0.7454 (tt0) REVERT: A 317 MET cc_start: 0.6932 (mtp) cc_final: 0.6531 (mtp) REVERT: B 25 GLN cc_start: 0.7781 (tt0) cc_final: 0.7454 (tt0) REVERT: B 60 TRP cc_start: 0.8508 (p-90) cc_final: 0.8230 (p-90) REVERT: B 159 TRP cc_start: 0.8537 (m100) cc_final: 0.8179 (m100) REVERT: B 193 GLU cc_start: 0.7349 (mp0) cc_final: 0.6891 (mp0) REVERT: B 201 MET cc_start: 0.6755 (ttp) cc_final: 0.6454 (ttp) REVERT: B 262 THR cc_start: 0.7762 (t) cc_final: 0.7366 (p) REVERT: B 292 GLN cc_start: 0.7653 (tt0) cc_final: 0.7449 (tt0) REVERT: B 317 MET cc_start: 0.6935 (mtp) cc_final: 0.6534 (mtp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1745 time to fit residues: 24.3020 Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 175 GLN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6274 Z= 0.193 Angle : 0.593 5.656 8416 Z= 0.320 Chirality : 0.040 0.172 950 Planarity : 0.005 0.041 972 Dihedral : 19.867 163.603 1126 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.27 % Allowed : 7.62 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.32), residues: 724 helix: 1.83 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.87 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 176 HIS 0.005 0.002 HIS A 270 PHE 0.017 0.002 PHE A 301 TYR 0.016 0.001 TYR B 297 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.645 Fit side-chains REVERT: A 60 TRP cc_start: 0.8547 (p-90) cc_final: 0.8241 (p-90) REVERT: A 130 MET cc_start: 0.5733 (mtt) cc_final: 0.5389 (mtt) REVERT: A 159 TRP cc_start: 0.8539 (m100) cc_final: 0.8243 (m100) REVERT: A 193 GLU cc_start: 0.7435 (mp0) cc_final: 0.6855 (mp0) REVERT: A 201 MET cc_start: 0.6852 (ttp) cc_final: 0.6602 (mtp) REVERT: A 292 GLN cc_start: 0.7606 (tt0) cc_final: 0.7339 (tt0) REVERT: A 317 MET cc_start: 0.6834 (mtp) cc_final: 0.6498 (mtp) REVERT: B 25 GLN cc_start: 0.7722 (tt0) cc_final: 0.7508 (tt0) REVERT: B 60 TRP cc_start: 0.8544 (p-90) cc_final: 0.8238 (p-90) REVERT: B 130 MET cc_start: 0.5723 (mtt) cc_final: 0.5390 (mtt) REVERT: B 159 TRP cc_start: 0.8541 (m100) cc_final: 0.8242 (m100) REVERT: B 193 GLU cc_start: 0.7436 (mp0) cc_final: 0.6856 (mp0) REVERT: B 201 MET cc_start: 0.6863 (ttp) cc_final: 0.6613 (mtp) REVERT: B 292 GLN cc_start: 0.7601 (tt0) cc_final: 0.7334 (tt0) REVERT: B 317 MET cc_start: 0.6823 (mtp) cc_final: 0.6460 (mtp) outliers start: 8 outliers final: 8 residues processed: 91 average time/residue: 0.1628 time to fit residues: 20.4893 Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6274 Z= 0.162 Angle : 0.543 5.386 8416 Z= 0.296 Chirality : 0.039 0.133 950 Planarity : 0.005 0.039 972 Dihedral : 17.411 163.915 1126 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.59 % Allowed : 10.00 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.32), residues: 724 helix: 2.00 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.74 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 52 HIS 0.005 0.002 HIS A 270 PHE 0.013 0.001 PHE B 165 TYR 0.016 0.001 TYR A 297 ARG 0.002 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.760 Fit side-chains REVERT: A 60 TRP cc_start: 0.8572 (p-90) cc_final: 0.8244 (p-90) REVERT: A 130 MET cc_start: 0.5786 (mtt) cc_final: 0.5266 (mtt) REVERT: A 159 TRP cc_start: 0.8505 (m100) cc_final: 0.8206 (m100) REVERT: A 317 MET cc_start: 0.6899 (mtp) cc_final: 0.6520 (mtp) REVERT: A 355 MET cc_start: 0.6561 (ttp) cc_final: 0.6347 (ttp) REVERT: B 60 TRP cc_start: 0.8570 (p-90) cc_final: 0.8243 (p-90) REVERT: B 130 MET cc_start: 0.5780 (mtt) cc_final: 0.5261 (mtt) REVERT: B 159 TRP cc_start: 0.8505 (m100) cc_final: 0.8204 (m100) REVERT: B 317 MET cc_start: 0.6873 (mtp) cc_final: 0.6510 (mtp) REVERT: B 355 MET cc_start: 0.6559 (ttp) cc_final: 0.6341 (ttp) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.1469 time to fit residues: 17.8600 Evaluate side-chains 82 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 144 ASN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 242 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6274 Z= 0.265 Angle : 0.643 6.068 8416 Z= 0.346 Chirality : 0.042 0.181 950 Planarity : 0.005 0.038 972 Dihedral : 16.527 165.416 1126 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.86 % Allowed : 13.02 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 724 helix: 1.56 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 176 HIS 0.006 0.002 HIS A 270 PHE 0.027 0.002 PHE B 301 TYR 0.016 0.002 TYR A 282 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.703 Fit side-chains REVERT: A 60 TRP cc_start: 0.8627 (p-90) cc_final: 0.8285 (p-90) REVERT: A 130 MET cc_start: 0.5996 (mtt) cc_final: 0.5416 (mtt) REVERT: A 317 MET cc_start: 0.7044 (mtp) cc_final: 0.6715 (mtp) REVERT: A 355 MET cc_start: 0.6710 (ttp) cc_final: 0.6457 (ttp) REVERT: B 60 TRP cc_start: 0.8625 (p-90) cc_final: 0.8284 (p-90) REVERT: B 130 MET cc_start: 0.5996 (mtt) cc_final: 0.5419 (mtt) REVERT: B 355 MET cc_start: 0.6702 (ttp) cc_final: 0.6447 (ttp) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.1391 time to fit residues: 18.3273 Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 175 GLN B 242 ASN B 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6274 Z= 0.258 Angle : 0.629 6.320 8416 Z= 0.339 Chirality : 0.041 0.168 950 Planarity : 0.005 0.040 972 Dihedral : 16.331 165.178 1126 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.38 % Allowed : 16.35 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 724 helix: 1.52 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -2.74 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 52 HIS 0.006 0.002 HIS B 376 PHE 0.021 0.002 PHE B 301 TYR 0.015 0.002 TYR A 297 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.764 Fit side-chains REVERT: A 46 MET cc_start: 0.6822 (mmt) cc_final: 0.6205 (mmt) REVERT: A 60 TRP cc_start: 0.8680 (p-90) cc_final: 0.8408 (p-90) REVERT: A 130 MET cc_start: 0.6035 (mtt) cc_final: 0.5448 (mtt) REVERT: A 317 MET cc_start: 0.7012 (mtp) cc_final: 0.6683 (mtp) REVERT: A 355 MET cc_start: 0.6791 (ttp) cc_final: 0.6501 (ttp) REVERT: B 46 MET cc_start: 0.6804 (mmt) cc_final: 0.6190 (mmt) REVERT: B 60 TRP cc_start: 0.8678 (p-90) cc_final: 0.8407 (p-90) REVERT: B 130 MET cc_start: 0.5985 (mtt) cc_final: 0.5388 (mtt) REVERT: B 355 MET cc_start: 0.6784 (ttp) cc_final: 0.6493 (ttp) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.1418 time to fit residues: 17.5005 Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6274 Z= 0.224 Angle : 0.607 6.550 8416 Z= 0.327 Chirality : 0.040 0.158 950 Planarity : 0.005 0.040 972 Dihedral : 15.562 163.422 1126 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.70 % Allowed : 15.40 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.31), residues: 724 helix: 1.53 (0.23), residues: 482 sheet: -1.18 (1.02), residues: 24 loop : -2.78 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 52 HIS 0.005 0.002 HIS B 270 PHE 0.018 0.002 PHE B 301 TYR 0.015 0.002 TYR A 238 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.662 Fit side-chains REVERT: A 46 MET cc_start: 0.6868 (mmt) cc_final: 0.6239 (mmt) REVERT: A 60 TRP cc_start: 0.8690 (p-90) cc_final: 0.8411 (p-90) REVERT: A 130 MET cc_start: 0.6199 (mtt) cc_final: 0.5571 (mtt) REVERT: A 159 TRP cc_start: 0.8672 (m100) cc_final: 0.8227 (m100) REVERT: A 317 MET cc_start: 0.6985 (mtp) cc_final: 0.6659 (mtp) REVERT: A 355 MET cc_start: 0.6811 (ttp) cc_final: 0.6483 (ttp) REVERT: B 46 MET cc_start: 0.6851 (mmt) cc_final: 0.6224 (mmt) REVERT: B 60 TRP cc_start: 0.8688 (p-90) cc_final: 0.8411 (p-90) REVERT: B 130 MET cc_start: 0.6191 (mtt) cc_final: 0.5588 (mtt) REVERT: B 159 TRP cc_start: 0.8672 (m100) cc_final: 0.8225 (m100) REVERT: B 355 MET cc_start: 0.6801 (ttp) cc_final: 0.6473 (ttp) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.1452 time to fit residues: 19.1505 Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6274 Z= 0.196 Angle : 0.584 5.839 8416 Z= 0.317 Chirality : 0.039 0.154 950 Planarity : 0.005 0.040 972 Dihedral : 14.977 159.918 1126 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.27 % Allowed : 16.98 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 724 helix: 1.55 (0.23), residues: 486 sheet: -1.15 (1.02), residues: 24 loop : -2.82 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 52 HIS 0.006 0.002 HIS B 376 PHE 0.017 0.002 PHE A 165 TYR 0.015 0.001 TYR B 238 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.624 Fit side-chains REVERT: A 46 MET cc_start: 0.6801 (mmt) cc_final: 0.6138 (mmt) REVERT: A 60 TRP cc_start: 0.8676 (p-90) cc_final: 0.8405 (p-90) REVERT: A 130 MET cc_start: 0.6181 (mtt) cc_final: 0.5579 (mtt) REVERT: A 159 TRP cc_start: 0.8652 (m100) cc_final: 0.8232 (m100) REVERT: A 317 MET cc_start: 0.6943 (mtp) cc_final: 0.6684 (mtp) REVERT: A 355 MET cc_start: 0.6676 (ttp) cc_final: 0.6368 (ttp) REVERT: B 46 MET cc_start: 0.6784 (mmt) cc_final: 0.6123 (mmt) REVERT: B 60 TRP cc_start: 0.8674 (p-90) cc_final: 0.8403 (p-90) REVERT: B 130 MET cc_start: 0.6158 (mtt) cc_final: 0.5544 (mtt) REVERT: B 159 TRP cc_start: 0.8651 (m100) cc_final: 0.8232 (m100) REVERT: B 355 MET cc_start: 0.6674 (ttp) cc_final: 0.6354 (ttp) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.1456 time to fit residues: 17.3473 Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6274 Z= 0.203 Angle : 0.585 5.858 8416 Z= 0.317 Chirality : 0.039 0.158 950 Planarity : 0.005 0.040 972 Dihedral : 14.717 154.987 1126 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.59 % Allowed : 17.46 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.32), residues: 724 helix: 1.58 (0.23), residues: 482 sheet: -1.27 (1.03), residues: 24 loop : -2.68 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 52 HIS 0.006 0.002 HIS B 376 PHE 0.016 0.002 PHE B 165 TYR 0.015 0.001 TYR B 238 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.670 Fit side-chains REVERT: A 46 MET cc_start: 0.6743 (mmt) cc_final: 0.6123 (mmt) REVERT: A 60 TRP cc_start: 0.8703 (p-90) cc_final: 0.8432 (p-90) REVERT: A 130 MET cc_start: 0.6207 (mtt) cc_final: 0.5580 (mtt) REVERT: A 159 TRP cc_start: 0.8633 (m100) cc_final: 0.8232 (m100) REVERT: A 317 MET cc_start: 0.7094 (mtp) cc_final: 0.6809 (mtp) REVERT: A 355 MET cc_start: 0.6707 (ttp) cc_final: 0.6380 (ttp) REVERT: B 46 MET cc_start: 0.6725 (mmt) cc_final: 0.6108 (mmt) REVERT: B 60 TRP cc_start: 0.8698 (p-90) cc_final: 0.8428 (p-90) REVERT: B 130 MET cc_start: 0.6185 (mtt) cc_final: 0.5586 (mtt) REVERT: B 159 TRP cc_start: 0.8633 (m100) cc_final: 0.8230 (m100) REVERT: B 355 MET cc_start: 0.6702 (ttp) cc_final: 0.6371 (ttp) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.1388 time to fit residues: 17.1257 Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6274 Z= 0.172 Angle : 0.565 6.327 8416 Z= 0.309 Chirality : 0.040 0.187 950 Planarity : 0.005 0.040 972 Dihedral : 14.273 150.959 1126 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.95 % Allowed : 18.25 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.32), residues: 724 helix: 1.83 (0.23), residues: 472 sheet: -1.25 (1.00), residues: 24 loop : -2.77 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 52 HIS 0.006 0.002 HIS B 316 PHE 0.013 0.001 PHE B 165 TYR 0.016 0.001 TYR A 238 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.574 Fit side-chains REVERT: A 28 LYS cc_start: 0.5563 (mttt) cc_final: 0.5110 (tptm) REVERT: A 46 MET cc_start: 0.6723 (mmt) cc_final: 0.6403 (mmt) REVERT: A 60 TRP cc_start: 0.8682 (p-90) cc_final: 0.8359 (p-90) REVERT: A 130 MET cc_start: 0.6161 (mtt) cc_final: 0.5578 (mtt) REVERT: A 159 TRP cc_start: 0.8621 (m100) cc_final: 0.8224 (m100) REVERT: A 317 MET cc_start: 0.6986 (mtp) cc_final: 0.6716 (mtp) REVERT: A 355 MET cc_start: 0.6634 (ttp) cc_final: 0.6302 (ttp) REVERT: B 46 MET cc_start: 0.6709 (mmt) cc_final: 0.6387 (mmt) REVERT: B 60 TRP cc_start: 0.8680 (p-90) cc_final: 0.8360 (p-90) REVERT: B 130 MET cc_start: 0.6133 (mtt) cc_final: 0.5587 (mtt) REVERT: B 159 TRP cc_start: 0.8621 (m100) cc_final: 0.8223 (m100) REVERT: B 316 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.4646 (p-80) REVERT: B 355 MET cc_start: 0.6626 (ttp) cc_final: 0.6296 (ttp) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.1433 time to fit residues: 16.5743 Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 0.0030 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6274 Z= 0.183 Angle : 0.568 5.634 8416 Z= 0.310 Chirality : 0.039 0.168 950 Planarity : 0.005 0.040 972 Dihedral : 13.837 146.443 1126 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.95 % Allowed : 18.73 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.32), residues: 724 helix: 1.81 (0.23), residues: 482 sheet: -1.25 (1.00), residues: 24 loop : -2.60 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 52 HIS 0.005 0.002 HIS A 316 PHE 0.015 0.001 PHE A 165 TYR 0.016 0.001 TYR A 238 ARG 0.001 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.688 Fit side-chains REVERT: A 28 LYS cc_start: 0.5574 (mttt) cc_final: 0.5105 (tptm) REVERT: A 46 MET cc_start: 0.6690 (mmt) cc_final: 0.6376 (mmt) REVERT: A 60 TRP cc_start: 0.8691 (p-90) cc_final: 0.8363 (p-90) REVERT: A 130 MET cc_start: 0.6196 (mtt) cc_final: 0.5601 (mtt) REVERT: A 159 TRP cc_start: 0.8640 (m100) cc_final: 0.8245 (m100) REVERT: A 316 HIS cc_start: 0.5860 (OUTLIER) cc_final: 0.4667 (p-80) REVERT: A 317 MET cc_start: 0.7035 (mtp) cc_final: 0.6759 (mtp) REVERT: A 355 MET cc_start: 0.6676 (ttp) cc_final: 0.6349 (ttp) REVERT: B 46 MET cc_start: 0.6671 (mmt) cc_final: 0.6359 (mmt) REVERT: B 60 TRP cc_start: 0.8690 (p-90) cc_final: 0.8365 (p-90) REVERT: B 130 MET cc_start: 0.6176 (mtt) cc_final: 0.5615 (mtt) REVERT: B 159 TRP cc_start: 0.8640 (m100) cc_final: 0.8243 (m100) REVERT: B 316 HIS cc_start: 0.5857 (OUTLIER) cc_final: 0.4632 (p-80) REVERT: B 355 MET cc_start: 0.6671 (ttp) cc_final: 0.6341 (ttp) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.1461 time to fit residues: 17.2371 Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146051 restraints weight = 6451.252| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.53 r_work: 0.3375 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6274 Z= 0.233 Angle : 0.616 10.319 8416 Z= 0.331 Chirality : 0.041 0.166 950 Planarity : 0.005 0.040 972 Dihedral : 13.973 144.820 1126 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.43 % Allowed : 18.41 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.32), residues: 724 helix: 1.58 (0.23), residues: 484 sheet: -1.25 (1.02), residues: 24 loop : -2.41 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 52 HIS 0.005 0.002 HIS A 270 PHE 0.018 0.002 PHE B 301 TYR 0.016 0.002 TYR A 238 ARG 0.001 0.000 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1343.31 seconds wall clock time: 25 minutes 32.58 seconds (1532.58 seconds total)