Starting phenix.real_space_refine on Thu Jan 18 02:26:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/01_2024/7ck6_30382_updated.pdb" } resolution = 3.4 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= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 32 5.16 5 C 4808 2.51 5 N 1281 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7460 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.09, per 1000 atoms: 0.55 Number of scatterers: 7460 At special positions: 0 Unit cell: (111.24, 145.8, 96.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 1 15.00 O 1338 8.00 N 1281 7.00 C 4808 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: 3.74 Conformation dependent library (CDL) restraints added in 2.6 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 4 sheets defined 34.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.045A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 89 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 90 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 91 removed outlier: 4.045A pdb=" N HIS B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS B 89 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS B 90 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 117 Proline residue: C 98 - end of helix removed outlier: 3.784A pdb=" N GLU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 95 Processing helix chain 'D' and resid 97 through 117 Processing helix chain 'E' and resid 24 through 34 Processing helix chain 'E' and resid 43 through 65 removed outlier: 3.509A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 34 Processing helix chain 'F' and resid 44 through 65 Processing helix chain 'G' and resid 7 through 36 removed outlier: 3.892A pdb=" N TRP G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 53' Processing helix chain 'H' and resid 7 through 36 removed outlier: 3.893A pdb=" N TRP H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'I' and resid 13 through 47 Proline residue: I 42 - end of helix removed outlier: 3.793A pdb=" N LYS I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 47 Proline residue: J 42 - end of helix removed outlier: 3.793A pdb=" N LYS J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.671A pdb=" N PHE A 301 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.731A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.670A pdb=" N PHE B 301 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.669A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1419 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: 2.44 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2343 1.33 - 1.45: 1063 1.45 - 1.57: 4157 1.57 - 1.69: 2 1.69 - 1.80: 56 Bond restraints: 7621 Sorted by residual: bond pdb=" C31 PC1 A 401 " pdb=" O31 PC1 A 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 PC1 A 401 " pdb=" O21 PC1 A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CA HIS A 347 " pdb=" C HIS A 347 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.33e+01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.32e+01 ... (remaining 7616 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 210 106.47 - 113.36: 4152 113.36 - 120.25: 2742 120.25 - 127.14: 3105 127.14 - 134.03: 90 Bond angle restraints: 10299 Sorted by residual: angle pdb=" N PRO A 333 " pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 110.70 124.06 -13.36 1.22e+00 6.72e-01 1.20e+02 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 124.05 -13.35 1.22e+00 6.72e-01 1.20e+02 angle pdb=" C GLU H 46 " pdb=" N PRO H 47 " pdb=" CA PRO H 47 " ideal model delta sigma weight residual 119.84 132.57 -12.73 1.25e+00 6.40e-01 1.04e+02 angle pdb=" C GLU G 46 " pdb=" N PRO G 47 " pdb=" CA PRO G 47 " ideal model delta sigma weight residual 119.84 132.41 -12.57 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR B 292 " pdb=" CA THR B 292 " pdb=" C THR B 292 " ideal model delta sigma weight residual 111.14 119.93 -8.79 1.08e+00 8.57e-01 6.62e+01 ... (remaining 10294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 3951 15.13 - 30.26: 468 30.26 - 45.39: 82 45.39 - 60.51: 24 60.51 - 75.64: 7 Dihedral angle restraints: 4532 sinusoidal: 1864 harmonic: 2668 Sorted by residual: dihedral pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CA GLN A 182 " pdb=" CB GLN A 182 " ideal model delta harmonic sigma weight residual 122.80 134.05 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" C GLN B 182 " pdb=" N GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1029 0.096 - 0.192: 96 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.480: 2 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLN B 182 " pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CB GLN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA GLN A 182 " pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CB GLN A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1140 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 46 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO H 47 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 47 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 46 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 47 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 47 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 66 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR C 66 " 0.044 2.00e-02 2.50e+03 pdb=" O THR C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 3719 2.95 - 3.60: 10420 3.60 - 4.25: 14270 4.25 - 4.90: 25387 Nonbonded interactions: 53825 Sorted by model distance: nonbonded pdb=" O ASN F 39 " pdb=" CE2 PHE F 41 " model vdw 1.652 3.340 nonbonded pdb=" O LEU H 30 " pdb=" CD2 LEU H 34 " model vdw 1.677 3.460 nonbonded pdb=" O ASP F 37 " pdb=" OD1 ASP F 40 " model vdw 1.722 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" ND2 ASN F 48 " model vdw 1.824 2.520 nonbonded pdb=" O LEU G 30 " pdb=" CD2 LEU G 34 " model vdw 1.843 3.460 ... (remaining 53820 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 77 through 360) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.220 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: 3.830 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 0.125 7621 Z= 0.508 Angle : 1.142 13.363 10299 Z= 0.740 Chirality : 0.065 0.480 1143 Planarity : 0.005 0.065 1310 Dihedral : 13.465 75.643 2816 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 36.32 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.12 % Rotamer: Outliers : 4.12 % Allowed : 12.38 % Favored : 83.50 % Cbeta Deviations : 0.23 % 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: 0.38 (0.28), residues: 916 helix: 2.24 (0.30), residues: 300 sheet: 0.39 (0.27), residues: 378 loop : -2.66 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.003 0.001 HIS A 220 PHE 0.031 0.002 PHE A 344 TYR 0.018 0.002 TYR A 129 ARG 0.004 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ASP cc_start: 0.7206 (m-30) cc_final: 0.6706 (m-30) REVERT: C 97 LEU cc_start: 0.8892 (tp) cc_final: 0.8643 (tp) REVERT: C 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9088 (mt) REVERT: I 38 LEU cc_start: 0.9032 (mm) cc_final: 0.8766 (mm) outliers start: 33 outliers final: 12 residues processed: 319 average time/residue: 0.2805 time to fit residues: 108.2601 Evaluate side-chains 178 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 220 HIS A 223 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 182 GLN B 220 HIS B 223 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN E 23 ASN E 48 ASN E 61 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 61 ASN G 10 GLN H 10 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7621 Z= 0.245 Angle : 0.881 11.999 10299 Z= 0.429 Chirality : 0.048 0.323 1143 Planarity : 0.006 0.057 1310 Dihedral : 7.692 54.102 1070 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 5.25 % Allowed : 20.75 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 916 helix: 3.02 (0.28), residues: 292 sheet: 1.02 (0.26), residues: 376 loop : -2.51 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 54 HIS 0.005 0.001 HIS A 112 PHE 0.020 0.002 PHE C 101 TYR 0.018 0.002 TYR I 34 ARG 0.008 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 LEU cc_start: 0.8847 (tp) cc_final: 0.8575 (tp) REVERT: I 17 LYS cc_start: 0.9594 (mttt) cc_final: 0.9212 (mtmt) REVERT: I 31 PHE cc_start: 0.8883 (t80) cc_final: 0.8658 (t80) REVERT: J 17 LYS cc_start: 0.9547 (mttt) cc_final: 0.9128 (mtmt) REVERT: J 31 PHE cc_start: 0.8938 (t80) cc_final: 0.8703 (t80) outliers start: 42 outliers final: 19 residues processed: 217 average time/residue: 0.1797 time to fit residues: 51.7732 Evaluate side-chains 185 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7621 Z= 0.246 Angle : 0.853 11.293 10299 Z= 0.406 Chirality : 0.049 0.257 1143 Planarity : 0.005 0.048 1310 Dihedral : 7.237 57.103 1055 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 5.50 % Allowed : 21.25 % Favored : 73.25 % 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: 1.14 (0.28), residues: 916 helix: 2.79 (0.29), residues: 300 sheet: 0.96 (0.25), residues: 376 loop : -2.40 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.026 0.002 PHE C 101 TYR 0.030 0.001 TYR J 34 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 LEU cc_start: 0.8543 (mp) cc_final: 0.8312 (tt) REVERT: B 294 MET cc_start: 0.8243 (tpt) cc_final: 0.7860 (tpt) REVERT: E 64 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7099 (t70) REVERT: I 17 LYS cc_start: 0.9430 (mttt) cc_final: 0.9207 (mtmt) outliers start: 44 outliers final: 27 residues processed: 204 average time/residue: 0.1815 time to fit residues: 49.1479 Evaluate side-chains 181 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 0.0040 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 97 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 113 GLN C 116 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7621 Z= 0.270 Angle : 0.909 12.664 10299 Z= 0.424 Chirality : 0.048 0.227 1143 Planarity : 0.005 0.045 1310 Dihedral : 7.297 58.762 1055 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.24 % Favored : 94.43 % Rotamer: Outliers : 5.25 % Allowed : 24.00 % Favored : 70.75 % 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: 1.03 (0.28), residues: 916 helix: 2.56 (0.29), residues: 300 sheet: 0.94 (0.25), residues: 376 loop : -2.35 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.023 0.002 PHE J 31 TYR 0.015 0.002 TYR J 34 ARG 0.012 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7039 (ttm) REVERT: A 154 MET cc_start: 0.6807 (tpt) cc_final: 0.6586 (tpt) REVERT: B 280 ASP cc_start: 0.7931 (p0) cc_final: 0.7649 (p0) REVERT: C 108 MET cc_start: 0.8879 (mmp) cc_final: 0.8647 (mmp) REVERT: E 64 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7207 (t70) REVERT: F 64 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6972 (t70) REVERT: J 29 ARG cc_start: 0.8987 (mtm180) cc_final: 0.8766 (mpp80) outliers start: 42 outliers final: 30 residues processed: 181 average time/residue: 0.1923 time to fit residues: 46.2477 Evaluate side-chains 187 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7621 Z= 0.221 Angle : 0.891 13.884 10299 Z= 0.406 Chirality : 0.047 0.252 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.186 59.397 1053 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.00 % Allowed : 26.62 % Favored : 69.38 % 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: 1.01 (0.29), residues: 916 helix: 2.48 (0.30), residues: 300 sheet: 0.92 (0.26), residues: 378 loop : -2.28 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.021 0.002 PHE H 27 TYR 0.016 0.002 TYR I 34 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6839 (tpt) cc_final: 0.6639 (tpt) REVERT: A 280 ASP cc_start: 0.7906 (p0) cc_final: 0.7633 (p0) REVERT: B 280 ASP cc_start: 0.7866 (p0) cc_final: 0.7418 (p0) REVERT: B 296 ASP cc_start: 0.6776 (p0) cc_final: 0.6557 (p0) REVERT: E 64 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7137 (t70) REVERT: F 64 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6973 (t70) REVERT: I 29 ARG cc_start: 0.9016 (mtm180) cc_final: 0.8543 (mtm180) REVERT: J 29 ARG cc_start: 0.8995 (mtm180) cc_final: 0.8733 (mpp80) outliers start: 32 outliers final: 22 residues processed: 184 average time/residue: 0.1873 time to fit residues: 46.1359 Evaluate side-chains 182 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.0020 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7621 Z= 0.200 Angle : 0.920 15.782 10299 Z= 0.412 Chirality : 0.048 0.330 1143 Planarity : 0.005 0.051 1310 Dihedral : 7.046 59.741 1052 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 4.00 % Allowed : 27.00 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 916 helix: 2.42 (0.30), residues: 300 sheet: 1.00 (0.26), residues: 378 loop : -2.26 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.004 0.001 HIS B 238 PHE 0.021 0.001 PHE E 41 TYR 0.024 0.001 TYR J 34 ARG 0.003 0.001 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6702 (tpt) cc_final: 0.6498 (tpt) REVERT: A 280 ASP cc_start: 0.7946 (p0) cc_final: 0.7542 (p0) REVERT: B 280 ASP cc_start: 0.7907 (p0) cc_final: 0.7409 (p0) REVERT: B 296 ASP cc_start: 0.6711 (p0) cc_final: 0.6458 (p0) REVERT: E 64 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7207 (t70) REVERT: F 64 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6993 (t70) REVERT: I 29 ARG cc_start: 0.9028 (mtm180) cc_final: 0.8512 (mtm180) REVERT: J 29 ARG cc_start: 0.9022 (mtm180) cc_final: 0.8541 (mtm180) outliers start: 32 outliers final: 25 residues processed: 179 average time/residue: 0.1825 time to fit residues: 43.1387 Evaluate side-chains 185 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7621 Z= 0.266 Angle : 0.912 13.448 10299 Z= 0.417 Chirality : 0.048 0.286 1143 Planarity : 0.005 0.051 1310 Dihedral : 7.310 59.845 1052 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.88 % Allowed : 27.88 % Favored : 68.25 % 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: 0.92 (0.29), residues: 916 helix: 2.30 (0.30), residues: 306 sheet: 0.92 (0.26), residues: 378 loop : -2.37 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 57 HIS 0.005 0.001 HIS A 130 PHE 0.022 0.002 PHE E 41 TYR 0.025 0.002 TYR I 34 ARG 0.004 0.001 ARG J 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8052 (p0) cc_final: 0.7582 (p0) REVERT: B 280 ASP cc_start: 0.7991 (p0) cc_final: 0.7502 (p0) REVERT: B 296 ASP cc_start: 0.6687 (p0) cc_final: 0.6429 (p0) REVERT: E 64 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7173 (t70) REVERT: F 64 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6989 (t70) outliers start: 31 outliers final: 24 residues processed: 175 average time/residue: 0.1921 time to fit residues: 44.3578 Evaluate side-chains 178 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7621 Z= 0.250 Angle : 0.936 14.834 10299 Z= 0.421 Chirality : 0.050 0.328 1143 Planarity : 0.005 0.049 1310 Dihedral : 7.202 57.037 1052 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.62 % Allowed : 28.00 % Favored : 67.38 % 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: 0.89 (0.29), residues: 916 helix: 2.23 (0.29), residues: 306 sheet: 0.96 (0.26), residues: 376 loop : -2.40 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 259 HIS 0.003 0.001 HIS B 238 PHE 0.024 0.002 PHE E 41 TYR 0.014 0.001 TYR J 34 ARG 0.003 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8043 (p0) cc_final: 0.7556 (p0) REVERT: B 235 LEU cc_start: 0.8618 (tt) cc_final: 0.8199 (tp) REVERT: B 280 ASP cc_start: 0.8020 (p0) cc_final: 0.7524 (p0) REVERT: B 296 ASP cc_start: 0.6433 (p0) cc_final: 0.6109 (p0) REVERT: E 64 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7189 (t70) REVERT: F 64 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6974 (t70) outliers start: 37 outliers final: 29 residues processed: 179 average time/residue: 0.1960 time to fit residues: 46.9273 Evaluate side-chains 182 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7621 Z= 0.219 Angle : 0.955 15.644 10299 Z= 0.426 Chirality : 0.049 0.362 1143 Planarity : 0.005 0.052 1310 Dihedral : 7.080 56.292 1052 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.00 % Allowed : 28.62 % Favored : 67.38 % 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: 0.98 (0.29), residues: 916 helix: 2.30 (0.30), residues: 306 sheet: 1.01 (0.27), residues: 376 loop : -2.35 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.015 0.001 HIS B 130 PHE 0.024 0.001 PHE E 41 TYR 0.016 0.001 TYR J 34 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8027 (p0) cc_final: 0.7531 (p0) REVERT: B 280 ASP cc_start: 0.7953 (p0) cc_final: 0.7435 (p0) REVERT: B 296 ASP cc_start: 0.6429 (p0) cc_final: 0.6086 (p0) REVERT: E 32 TYR cc_start: 0.8644 (t80) cc_final: 0.8342 (t80) REVERT: E 64 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7059 (t70) REVERT: F 39 ASN cc_start: 0.8342 (m-40) cc_final: 0.7770 (p0) REVERT: F 64 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6960 (t70) outliers start: 32 outliers final: 24 residues processed: 178 average time/residue: 0.1922 time to fit residues: 45.4449 Evaluate side-chains 178 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7621 Z= 0.320 Angle : 0.985 15.310 10299 Z= 0.455 Chirality : 0.051 0.339 1143 Planarity : 0.005 0.051 1310 Dihedral : 7.304 57.223 1052 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.50 % Allowed : 29.75 % Favored : 66.75 % 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: 0.90 (0.29), residues: 916 helix: 2.26 (0.30), residues: 294 sheet: 0.95 (0.27), residues: 376 loop : -2.14 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 259 HIS 0.005 0.001 HIS A 166 PHE 0.037 0.002 PHE C 101 TYR 0.066 0.002 TYR J 34 ARG 0.004 0.001 ARG A 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8177 (p0) cc_final: 0.7691 (p0) REVERT: B 280 ASP cc_start: 0.8123 (p0) cc_final: 0.7653 (p0) REVERT: B 296 ASP cc_start: 0.6420 (p0) cc_final: 0.6042 (p0) REVERT: I 29 ARG cc_start: 0.8999 (mtm180) cc_final: 0.8606 (mtm110) outliers start: 28 outliers final: 24 residues processed: 165 average time/residue: 0.1815 time to fit residues: 40.5945 Evaluate side-chains 170 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.069883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052021 restraints weight = 32455.397| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 5.16 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7621 Z= 0.231 Angle : 1.019 16.620 10299 Z= 0.455 Chirality : 0.052 0.388 1143 Planarity : 0.005 0.051 1310 Dihedral : 7.011 58.016 1052 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.38 % Allowed : 29.38 % Favored : 67.25 % 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: 1.01 (0.29), residues: 916 helix: 2.35 (0.30), residues: 294 sheet: 1.01 (0.27), residues: 376 loop : -2.10 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 57 HIS 0.003 0.001 HIS B 130 PHE 0.039 0.002 PHE C 101 TYR 0.062 0.002 TYR I 34 ARG 0.005 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.49 seconds wall clock time: 43 minutes 49.59 seconds (2629.59 seconds total)