Starting phenix.real_space_refine on Thu Mar 14 20:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/03_2024/7x58_33011.pdb" } resolution = 3.93 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= 1.000 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 242 5.49 5 S 20 5.16 5 C 5377 2.51 5 N 1846 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9775 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.63, per 1000 atoms: 0.58 Number of scatterers: 9775 At special positions: 0 Unit cell: (121.8, 95.55, 110.25, 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 20 16.00 P 242 15.00 O 2290 8.00 N 1846 7.00 C 5377 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: 5.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 79.9% alpha, 2.3% beta 117 base pairs and 201 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.748A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.674A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.542A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.529A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.511A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.848A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.793A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.637A pdb=" N ILE C 119 " --> pdb=" O ARG D 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.198A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.666A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 119 357 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 303 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 201 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 5.57 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: 1842 1.33 - 1.45: 3403 1.45 - 1.57: 4667 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10426 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CG LEU B 62 " pdb=" CD2 LEU B 62 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" C MET C 120 " pdb=" N PRO C 121 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.51e-02 4.39e+03 9.46e-01 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 99.35 - 105.97: 1336 105.97 - 112.58: 5606 112.58 - 119.20: 2725 119.20 - 125.81: 4635 125.81 - 132.43: 795 Bond angle restraints: 15097 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 112.43 109.34 3.09 9.20e-01 1.18e+00 1.13e+01 angle pdb=" CA ARG A 131 " pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " ideal model delta sigma weight residual 111.30 104.47 6.83 2.30e+00 1.89e-01 8.82e+00 angle pdb=" C ALA C 114 " pdb=" N LYS C 115 " pdb=" CA LYS C 115 " ideal model delta sigma weight residual 122.61 126.28 -3.67 1.56e+00 4.11e-01 5.54e+00 angle pdb=" C ARG D 78 " pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 121.54 125.74 -4.20 1.91e+00 2.74e-01 4.85e+00 ... (remaining 15092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 4570 35.47 - 70.94: 1069 70.94 - 106.41: 11 106.41 - 141.88: 1 141.88 - 177.36: 3 Dihedral angle restraints: 5654 sinusoidal: 3922 harmonic: 1732 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual -140.00 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 53.77 166.23 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 74.13 145.87 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 5651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1612 0.062 - 0.124: 104 0.124 - 0.185: 6 0.185 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CG LEU H 62 " pdb=" CB LEU H 62 " pdb=" CD1 LEU H 62 " pdb=" CD2 LEU H 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG A 131 " pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CB ARG A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1721 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 32 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 31 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO H 32 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 66 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.015 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1171 2.76 - 3.29: 8687 3.29 - 3.83: 19177 3.83 - 4.36: 22265 4.36 - 4.90: 30841 Nonbonded interactions: 82141 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.221 2.440 nonbonded pdb=" NH2 ARG G 63 " pdb=" OP1 DA I 18 " model vdw 2.267 2.520 nonbonded pdb=" O2 DT I -24 " pdb=" N2 DG J 25 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.293 2.520 nonbonded pdb=" NH2 ARG C 72 " pdb=" OP1 DC I -54 " model vdw 2.345 2.520 ... (remaining 82136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 95) selection = chain 'D' selection = chain 'F' selection = (chain 'H' and resid 24 through 95) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.780 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.320 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.003 0.041 10426 Z= 0.176 Angle : 0.565 6.829 15097 Z= 0.367 Chirality : 0.032 0.309 1724 Planarity : 0.003 0.033 1074 Dihedral : 27.062 177.356 4526 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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 (0.29), residues: 580 helix: 1.04 (0.21), residues: 434 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 113 PHE 0.013 0.001 PHE H 61 TYR 0.004 0.001 TYR B 88 ARG 0.003 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8253 (t0) cc_final: 0.8051 (t70) REVERT: A 87 SER cc_start: 0.9347 (m) cc_final: 0.9085 (t) REVERT: A 90 MET cc_start: 0.8113 (mmm) cc_final: 0.7792 (mmp) REVERT: B 31 LYS cc_start: 0.9128 (tttt) cc_final: 0.8903 (ttmm) REVERT: C 113 HIS cc_start: 0.9068 (t70) cc_final: 0.8687 (t-170) REVERT: C 126 LEU cc_start: 0.8913 (tp) cc_final: 0.8582 (tp) REVERT: D 53 GLU cc_start: 0.8764 (tp30) cc_final: 0.8490 (tp30) REVERT: D 84 MET cc_start: 0.8110 (tpp) cc_final: 0.7858 (tpp) REVERT: D 91 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7739 (mtpt) REVERT: E 90 MET cc_start: 0.8014 (ttt) cc_final: 0.7336 (tmm) REVERT: F 32 PRO cc_start: 0.9228 (Cg_exo) cc_final: 0.8930 (Cg_endo) REVERT: F 79 LYS cc_start: 0.8776 (mttm) cc_final: 0.8375 (tptp) REVERT: F 87 VAL cc_start: 0.8283 (t) cc_final: 0.8061 (t) REVERT: F 91 LYS cc_start: 0.8504 (mttt) cc_final: 0.8160 (mtpt) REVERT: G 81 ASP cc_start: 0.8219 (t0) cc_final: 0.7963 (t70) REVERT: G 107 THR cc_start: 0.9274 (m) cc_final: 0.8713 (p) REVERT: H 31 LYS cc_start: 0.9110 (tttt) cc_final: 0.8857 (ttmm) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3435 time to fit residues: 121.8417 Evaluate side-chains 169 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 64 ASN F 75 HIS G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10426 Z= 0.300 Angle : 0.652 9.176 15097 Z= 0.378 Chirality : 0.036 0.150 1724 Planarity : 0.005 0.055 1074 Dihedral : 31.501 174.638 3290 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 5.34 % Allowed : 21.15 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.33), residues: 580 helix: 2.62 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS E 113 PHE 0.011 0.002 PHE E 78 TYR 0.015 0.001 TYR B 88 ARG 0.010 0.001 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 74 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9148 (tt) REVERT: A 87 SER cc_start: 0.9356 (m) cc_final: 0.8946 (t) REVERT: C 90 MET cc_start: 0.7553 (tpp) cc_final: 0.7018 (tpp) REVERT: C 105 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8011 (mt-10) REVERT: C 120 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7973 (mmt) REVERT: D 52 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 84 MET cc_start: 0.8306 (tpp) cc_final: 0.7982 (tpp) REVERT: D 91 LYS cc_start: 0.8434 (tmtt) cc_final: 0.7790 (mtmm) REVERT: E 73 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8366 (tm-30) REVERT: E 90 MET cc_start: 0.7831 (ttt) cc_final: 0.7364 (tmm) REVERT: E 93 GLN cc_start: 0.8781 (tp40) cc_final: 0.8442 (tp40) REVERT: E 105 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7912 (mt-10) REVERT: E 112 ILE cc_start: 0.9465 (tp) cc_final: 0.9260 (pt) REVERT: E 120 MET cc_start: 0.8557 (mtp) cc_final: 0.8287 (mtp) REVERT: F 32 PRO cc_start: 0.9216 (Cg_exo) cc_final: 0.8989 (Cg_endo) REVERT: F 53 GLU cc_start: 0.8740 (tp30) cc_final: 0.8464 (tp30) REVERT: F 79 LYS cc_start: 0.8977 (mttm) cc_final: 0.8337 (tptp) REVERT: F 84 MET cc_start: 0.8084 (mmm) cc_final: 0.7314 (tpp) REVERT: F 91 LYS cc_start: 0.8628 (mttt) cc_final: 0.8097 (mtpt) REVERT: G 90 MET cc_start: 0.8771 (mmp) cc_final: 0.8191 (tpt) REVERT: G 120 MET cc_start: 0.8618 (mmm) cc_final: 0.7965 (mmt) REVERT: H 52 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7663 (tm-30) outliers start: 27 outliers final: 16 residues processed: 205 average time/residue: 0.2595 time to fit residues: 69.4928 Evaluate side-chains 175 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10426 Z= 0.437 Angle : 0.730 8.275 15097 Z= 0.421 Chirality : 0.040 0.168 1724 Planarity : 0.005 0.033 1074 Dihedral : 32.479 174.674 3290 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 10.08 % Allowed : 22.92 % Favored : 67.00 % 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: 2.25 (0.33), residues: 580 helix: 2.38 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.93 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS D 75 PHE 0.018 0.003 PHE C 104 TYR 0.009 0.002 TYR D 72 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9409 (m) cc_final: 0.9079 (t) REVERT: A 90 MET cc_start: 0.8511 (tpt) cc_final: 0.8140 (tpp) REVERT: A 120 MET cc_start: 0.8533 (mmm) cc_final: 0.8317 (mmm) REVERT: A 125 GLN cc_start: 0.8631 (mt0) cc_final: 0.8298 (mt0) REVERT: A 134 ARG cc_start: 0.7148 (mmp-170) cc_final: 0.6917 (mmp-170) REVERT: B 52 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 79 LYS cc_start: 0.9078 (mttm) cc_final: 0.8871 (tttt) REVERT: C 90 MET cc_start: 0.7522 (tpp) cc_final: 0.6791 (tpp) REVERT: C 105 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 109 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8622 (mm) REVERT: D 67 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8369 (ttp80) REVERT: D 84 MET cc_start: 0.8302 (tpp) cc_final: 0.8012 (tpp) REVERT: E 90 MET cc_start: 0.8130 (ttt) cc_final: 0.7440 (tmm) REVERT: E 105 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8092 (mt-10) REVERT: E 120 MET cc_start: 0.8839 (mtp) cc_final: 0.8106 (mtp) REVERT: F 32 PRO cc_start: 0.9208 (Cg_exo) cc_final: 0.8940 (Cg_endo) REVERT: F 53 GLU cc_start: 0.8863 (tp30) cc_final: 0.8642 (tp30) REVERT: F 68 ASP cc_start: 0.8335 (m-30) cc_final: 0.7810 (t70) REVERT: F 79 LYS cc_start: 0.9086 (mttm) cc_final: 0.8430 (tptp) REVERT: F 84 MET cc_start: 0.8182 (mmm) cc_final: 0.7552 (tpp) REVERT: F 91 LYS cc_start: 0.8668 (mttt) cc_final: 0.8313 (mtmt) REVERT: F 92 ARG cc_start: 0.7917 (mpt180) cc_final: 0.7522 (mtt90) REVERT: G 90 MET cc_start: 0.8876 (mmp) cc_final: 0.8412 (tpp) REVERT: G 93 GLN cc_start: 0.9369 (tt0) cc_final: 0.9122 (tt0) REVERT: G 107 THR cc_start: 0.9130 (m) cc_final: 0.8724 (p) REVERT: G 125 GLN cc_start: 0.8678 (mt0) cc_final: 0.8394 (mt0) REVERT: H 52 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7643 (tm-30) REVERT: H 79 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8719 (ttmm) REVERT: H 80 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9076 (p) outliers start: 51 outliers final: 32 residues processed: 201 average time/residue: 0.2591 time to fit residues: 68.2520 Evaluate side-chains 193 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 75 HIS G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.220 Angle : 0.609 7.035 15097 Z= 0.359 Chirality : 0.034 0.139 1724 Planarity : 0.004 0.032 1074 Dihedral : 32.085 174.929 3290 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.94 % Allowed : 29.25 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.34), residues: 580 helix: 2.82 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.86 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 75 PHE 0.011 0.001 PHE E 78 TYR 0.010 0.002 TYR B 88 ARG 0.005 0.001 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9360 (m) cc_final: 0.9022 (t) REVERT: A 120 MET cc_start: 0.8561 (mmm) cc_final: 0.8203 (mmm) REVERT: A 123 ASP cc_start: 0.9209 (m-30) cc_final: 0.8850 (m-30) REVERT: B 52 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 63 GLU cc_start: 0.7769 (tt0) cc_final: 0.7511 (tt0) REVERT: C 90 MET cc_start: 0.7522 (tpp) cc_final: 0.6731 (tpp) REVERT: C 105 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 29 ILE cc_start: 0.8577 (mm) cc_final: 0.8128 (mm) REVERT: D 88 TYR cc_start: 0.7504 (t80) cc_final: 0.7001 (t80) REVERT: D 91 LYS cc_start: 0.8531 (tmtt) cc_final: 0.7874 (ptmm) REVERT: E 90 MET cc_start: 0.8011 (ttt) cc_final: 0.7519 (tpp) REVERT: E 105 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 120 MET cc_start: 0.8607 (mtp) cc_final: 0.8396 (mtp) REVERT: F 32 PRO cc_start: 0.9102 (Cg_exo) cc_final: 0.8818 (Cg_endo) REVERT: F 68 ASP cc_start: 0.8240 (m-30) cc_final: 0.7661 (t0) REVERT: F 74 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7955 (tm-30) REVERT: F 79 LYS cc_start: 0.9130 (mttm) cc_final: 0.8432 (tptp) REVERT: F 84 MET cc_start: 0.8110 (mmm) cc_final: 0.7674 (tpp) REVERT: F 87 VAL cc_start: 0.8400 (t) cc_final: 0.8148 (t) REVERT: F 90 LEU cc_start: 0.8678 (tp) cc_final: 0.8243 (tt) REVERT: F 91 LYS cc_start: 0.8503 (mttt) cc_final: 0.8218 (mtpt) REVERT: G 90 MET cc_start: 0.8858 (mmp) cc_final: 0.8410 (tpt) REVERT: G 107 THR cc_start: 0.9222 (m) cc_final: 0.8916 (p) REVERT: G 120 MET cc_start: 0.8613 (mmm) cc_final: 0.7778 (mmt) REVERT: G 123 ASP cc_start: 0.9210 (m-30) cc_final: 0.8790 (m-30) REVERT: G 125 GLN cc_start: 0.8515 (mt0) cc_final: 0.8257 (mt0) REVERT: H 52 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7448 (tm-30) REVERT: H 79 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8677 (ttmm) outliers start: 25 outliers final: 15 residues processed: 204 average time/residue: 0.2453 time to fit residues: 66.4468 Evaluate side-chains 181 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 GLN C 125 GLN D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.247 Angle : 0.624 7.956 15097 Z= 0.363 Chirality : 0.035 0.171 1724 Planarity : 0.004 0.034 1074 Dihedral : 32.062 175.286 3290 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 6.13 % Allowed : 30.83 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.34), residues: 580 helix: 2.85 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 75 PHE 0.010 0.001 PHE G 67 TYR 0.011 0.001 TYR H 88 ARG 0.005 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.9365 (m) cc_final: 0.9029 (t) REVERT: A 97 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7972 (tt0) REVERT: A 120 MET cc_start: 0.8568 (mmm) cc_final: 0.7659 (mmt) REVERT: A 123 ASP cc_start: 0.9215 (m-30) cc_final: 0.8975 (m-30) REVERT: B 52 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 63 GLU cc_start: 0.7796 (tt0) cc_final: 0.7534 (tt0) REVERT: C 90 MET cc_start: 0.7573 (tpp) cc_final: 0.6787 (tpp) REVERT: C 93 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8045 (tp40) REVERT: C 105 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8077 (mt-10) REVERT: D 29 ILE cc_start: 0.8604 (mm) cc_final: 0.8167 (mm) REVERT: D 88 TYR cc_start: 0.7366 (t80) cc_final: 0.7154 (t80) REVERT: D 90 LEU cc_start: 0.8601 (tp) cc_final: 0.8152 (tt) REVERT: D 91 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7723 (mtmm) REVERT: E 90 MET cc_start: 0.7988 (ttt) cc_final: 0.7740 (tpp) REVERT: E 105 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8114 (mt-10) REVERT: F 32 PRO cc_start: 0.9018 (Cg_exo) cc_final: 0.8718 (Cg_endo) REVERT: F 68 ASP cc_start: 0.8218 (m-30) cc_final: 0.7594 (t70) REVERT: F 79 LYS cc_start: 0.9152 (mttm) cc_final: 0.8439 (tptp) REVERT: F 84 MET cc_start: 0.8069 (mmm) cc_final: 0.7797 (tpp) REVERT: F 87 VAL cc_start: 0.8419 (t) cc_final: 0.8178 (t) REVERT: F 88 TYR cc_start: 0.8030 (m-10) cc_final: 0.7668 (m-10) REVERT: F 91 LYS cc_start: 0.8531 (mttt) cc_final: 0.8230 (mtpt) REVERT: G 90 MET cc_start: 0.8866 (mmp) cc_final: 0.8410 (tpt) REVERT: G 107 THR cc_start: 0.9222 (m) cc_final: 0.8914 (p) REVERT: G 120 MET cc_start: 0.8661 (mmm) cc_final: 0.7828 (mmt) REVERT: G 123 ASP cc_start: 0.9243 (m-30) cc_final: 0.8826 (m-30) REVERT: G 125 GLN cc_start: 0.8566 (mt0) cc_final: 0.8263 (mt0) REVERT: H 52 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7428 (tm-30) REVERT: H 63 GLU cc_start: 0.7792 (tt0) cc_final: 0.7587 (tt0) REVERT: H 79 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8664 (ttmm) outliers start: 31 outliers final: 21 residues processed: 191 average time/residue: 0.2471 time to fit residues: 63.1963 Evaluate side-chains 188 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.202 Angle : 0.604 8.060 15097 Z= 0.354 Chirality : 0.034 0.176 1724 Planarity : 0.004 0.031 1074 Dihedral : 31.892 175.915 3290 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 6.52 % Allowed : 30.63 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.33), residues: 580 helix: 2.79 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 75 PHE 0.009 0.001 PHE E 78 TYR 0.011 0.001 TYR B 88 ARG 0.007 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9331 (m) cc_final: 0.8972 (t) REVERT: A 120 MET cc_start: 0.8586 (mmm) cc_final: 0.7598 (mmt) REVERT: A 123 ASP cc_start: 0.9005 (m-30) cc_final: 0.8794 (m-30) REVERT: B 52 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 63 GLU cc_start: 0.7762 (tt0) cc_final: 0.7462 (tt0) REVERT: C 90 MET cc_start: 0.7509 (tpp) cc_final: 0.6763 (tpp) REVERT: C 105 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 29 ILE cc_start: 0.8611 (mm) cc_final: 0.8182 (mm) REVERT: D 90 LEU cc_start: 0.8647 (tp) cc_final: 0.8226 (tt) REVERT: E 90 MET cc_start: 0.7995 (ttt) cc_final: 0.7728 (tpp) REVERT: E 105 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8112 (mt-10) REVERT: F 32 PRO cc_start: 0.8944 (Cg_exo) cc_final: 0.8623 (Cg_endo) REVERT: F 68 ASP cc_start: 0.8117 (m-30) cc_final: 0.7543 (t70) REVERT: F 74 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: F 79 LYS cc_start: 0.9152 (mttm) cc_final: 0.8419 (tptp) REVERT: F 84 MET cc_start: 0.8090 (mmm) cc_final: 0.7859 (tpp) REVERT: F 87 VAL cc_start: 0.8395 (t) cc_final: 0.8160 (t) REVERT: F 88 TYR cc_start: 0.7976 (m-10) cc_final: 0.7655 (m-10) REVERT: F 90 LEU cc_start: 0.8629 (tp) cc_final: 0.8147 (tt) REVERT: F 91 LYS cc_start: 0.8490 (mttt) cc_final: 0.8190 (mtpt) REVERT: G 83 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7765 (mtp85) REVERT: G 90 MET cc_start: 0.8811 (mmp) cc_final: 0.8406 (tpt) REVERT: G 120 MET cc_start: 0.8618 (mmm) cc_final: 0.7909 (mmt) REVERT: H 52 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7336 (tm-30) REVERT: H 79 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8635 (ttmm) outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.2486 time to fit residues: 64.6721 Evaluate side-chains 187 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.202 Angle : 0.609 8.682 15097 Z= 0.354 Chirality : 0.034 0.175 1724 Planarity : 0.003 0.030 1074 Dihedral : 31.802 176.439 3290 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.55 % Allowed : 32.41 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.34), residues: 580 helix: 2.86 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 75 PHE 0.007 0.001 PHE G 67 TYR 0.009 0.001 TYR H 88 ARG 0.006 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9309 (m) cc_final: 0.8934 (t) REVERT: A 97 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8075 (tt0) REVERT: A 120 MET cc_start: 0.8445 (mmm) cc_final: 0.7968 (mmm) REVERT: A 123 ASP cc_start: 0.9006 (m-30) cc_final: 0.8730 (m-30) REVERT: B 52 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7394 (tm-30) REVERT: C 90 MET cc_start: 0.7606 (tpp) cc_final: 0.6748 (tpp) REVERT: C 105 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 29 ILE cc_start: 0.8603 (mm) cc_final: 0.8185 (mm) REVERT: D 88 TYR cc_start: 0.6926 (t80) cc_final: 0.6661 (t80) REVERT: D 90 LEU cc_start: 0.8604 (tp) cc_final: 0.8155 (tt) REVERT: D 91 LYS cc_start: 0.8374 (tmtt) cc_final: 0.7607 (mtmm) REVERT: E 90 MET cc_start: 0.7968 (ttt) cc_final: 0.7687 (tpp) REVERT: E 105 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 32 PRO cc_start: 0.8990 (Cg_exo) cc_final: 0.8655 (Cg_endo) REVERT: F 68 ASP cc_start: 0.8104 (m-30) cc_final: 0.7545 (t70) REVERT: F 74 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: F 79 LYS cc_start: 0.9113 (mttm) cc_final: 0.8426 (tptp) REVERT: F 84 MET cc_start: 0.8034 (mmm) cc_final: 0.7793 (tpp) REVERT: F 87 VAL cc_start: 0.8445 (t) cc_final: 0.8228 (t) REVERT: F 88 TYR cc_start: 0.7949 (m-10) cc_final: 0.7597 (m-10) REVERT: F 90 LEU cc_start: 0.8623 (tp) cc_final: 0.8143 (tt) REVERT: F 91 LYS cc_start: 0.8475 (mttt) cc_final: 0.8211 (mtpt) REVERT: G 61 LEU cc_start: 0.9484 (mt) cc_final: 0.9252 (mp) REVERT: G 90 MET cc_start: 0.8863 (mmp) cc_final: 0.8448 (tpt) REVERT: G 97 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7704 (mt-10) REVERT: G 120 MET cc_start: 0.8469 (mmm) cc_final: 0.7899 (mmt) REVERT: H 52 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7333 (tm-30) REVERT: H 79 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8616 (ttmm) outliers start: 23 outliers final: 18 residues processed: 191 average time/residue: 0.2462 time to fit residues: 62.2631 Evaluate side-chains 184 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 GLN C 125 GLN D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.230 Angle : 0.620 9.679 15097 Z= 0.358 Chirality : 0.034 0.177 1724 Planarity : 0.004 0.030 1074 Dihedral : 31.837 176.424 3290 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.74 % Allowed : 33.20 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.34), residues: 580 helix: 2.84 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.82 (0.39), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 75 PHE 0.009 0.001 PHE G 67 TYR 0.009 0.001 TYR D 88 ARG 0.007 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9342 (m) cc_final: 0.8979 (t) REVERT: A 120 MET cc_start: 0.8475 (mmm) cc_final: 0.7562 (mmt) REVERT: A 123 ASP cc_start: 0.9096 (m-30) cc_final: 0.8807 (m-30) REVERT: B 52 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 63 GLU cc_start: 0.7768 (tt0) cc_final: 0.7453 (tt0) REVERT: C 62 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8194 (mt) REVERT: C 90 MET cc_start: 0.7585 (tpp) cc_final: 0.6766 (tpp) REVERT: C 93 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: C 105 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 29 ILE cc_start: 0.8650 (mm) cc_final: 0.8238 (mm) REVERT: D 53 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8326 (mt-10) REVERT: D 88 TYR cc_start: 0.7074 (t80) cc_final: 0.6783 (t80) REVERT: D 90 LEU cc_start: 0.8598 (tp) cc_final: 0.8157 (tt) REVERT: D 91 LYS cc_start: 0.8405 (tmtt) cc_final: 0.7733 (mtmt) REVERT: E 90 MET cc_start: 0.7977 (ttt) cc_final: 0.7718 (tpp) REVERT: E 105 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8073 (mt-10) REVERT: E 125 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8337 (mm-40) REVERT: F 32 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8673 (Cg_endo) REVERT: F 53 GLU cc_start: 0.8294 (tt0) cc_final: 0.7964 (tt0) REVERT: F 68 ASP cc_start: 0.8144 (m-30) cc_final: 0.7564 (t70) REVERT: F 79 LYS cc_start: 0.9058 (mttm) cc_final: 0.8426 (tptp) REVERT: F 84 MET cc_start: 0.8060 (mmm) cc_final: 0.7724 (tpp) REVERT: F 87 VAL cc_start: 0.8424 (t) cc_final: 0.8195 (t) REVERT: F 88 TYR cc_start: 0.7946 (m-10) cc_final: 0.7554 (m-10) REVERT: F 90 LEU cc_start: 0.8658 (tp) cc_final: 0.8169 (tt) REVERT: F 91 LYS cc_start: 0.8463 (mttt) cc_final: 0.8209 (mtpt) REVERT: G 90 MET cc_start: 0.8885 (mmp) cc_final: 0.8474 (tpt) REVERT: G 120 MET cc_start: 0.8492 (mmm) cc_final: 0.7942 (mmt) REVERT: H 52 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7352 (tm-30) REVERT: H 79 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8632 (ttmm) outliers start: 24 outliers final: 21 residues processed: 181 average time/residue: 0.2448 time to fit residues: 58.9916 Evaluate side-chains 186 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10426 Z= 0.304 Angle : 0.664 10.274 15097 Z= 0.381 Chirality : 0.036 0.165 1724 Planarity : 0.004 0.034 1074 Dihedral : 32.064 175.661 3290 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.94 % Allowed : 33.40 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.34), residues: 580 helix: 2.77 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 75 PHE 0.013 0.002 PHE C 104 TYR 0.009 0.002 TYR C 99 ARG 0.008 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.9359 (m) cc_final: 0.9024 (t) REVERT: A 97 GLU cc_start: 0.8474 (tt0) cc_final: 0.8254 (tt0) REVERT: A 120 MET cc_start: 0.8453 (mmm) cc_final: 0.7745 (mmt) REVERT: B 52 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7600 (tm-30) REVERT: C 61 LEU cc_start: 0.9133 (mp) cc_final: 0.8919 (mp) REVERT: C 90 MET cc_start: 0.7620 (tpp) cc_final: 0.6738 (tpp) REVERT: C 97 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7897 (tt0) REVERT: C 105 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 88 TYR cc_start: 0.7006 (t80) cc_final: 0.6689 (t80) REVERT: D 90 LEU cc_start: 0.8543 (tp) cc_final: 0.8016 (tt) REVERT: D 91 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7787 (mtmt) REVERT: E 90 MET cc_start: 0.7954 (ttt) cc_final: 0.7739 (tpp) REVERT: E 105 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8180 (mt-10) REVERT: F 32 PRO cc_start: 0.8984 (Cg_exo) cc_final: 0.8674 (Cg_endo) REVERT: F 53 GLU cc_start: 0.8411 (tt0) cc_final: 0.8174 (tt0) REVERT: F 68 ASP cc_start: 0.8268 (m-30) cc_final: 0.7647 (t70) REVERT: F 79 LYS cc_start: 0.9041 (mttm) cc_final: 0.8464 (tptp) REVERT: F 84 MET cc_start: 0.8112 (mmm) cc_final: 0.7712 (tpp) REVERT: F 87 VAL cc_start: 0.8402 (t) cc_final: 0.8172 (t) REVERT: F 88 TYR cc_start: 0.7954 (m-10) cc_final: 0.7532 (m-10) REVERT: F 91 LYS cc_start: 0.8510 (mttt) cc_final: 0.8233 (mtpt) REVERT: G 90 MET cc_start: 0.8863 (mmp) cc_final: 0.8499 (tpt) REVERT: G 120 MET cc_start: 0.8492 (mmm) cc_final: 0.7861 (mmt) REVERT: H 52 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7523 (tm-30) REVERT: H 79 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8696 (ttmm) outliers start: 25 outliers final: 21 residues processed: 175 average time/residue: 0.2425 time to fit residues: 56.3690 Evaluate side-chains 172 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 19 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: D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.228 Angle : 0.649 10.911 15097 Z= 0.368 Chirality : 0.035 0.227 1724 Planarity : 0.004 0.032 1074 Dihedral : 31.863 176.278 3290 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.95 % Allowed : 35.18 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.33), residues: 580 helix: 2.83 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 75 PHE 0.011 0.001 PHE G 67 TYR 0.012 0.001 TYR B 88 ARG 0.007 0.000 ARG H 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9330 (m) cc_final: 0.8991 (t) REVERT: A 97 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: A 120 MET cc_start: 0.8490 (mmm) cc_final: 0.8115 (mmm) REVERT: A 123 ASP cc_start: 0.9090 (m-30) cc_final: 0.8780 (m-30) REVERT: B 52 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 90 MET cc_start: 0.7557 (tpp) cc_final: 0.6692 (tpp) REVERT: C 97 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7935 (tt0) REVERT: C 105 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 91 LYS cc_start: 0.8392 (tmtt) cc_final: 0.7742 (mtmt) REVERT: E 90 MET cc_start: 0.7960 (ttt) cc_final: 0.7519 (tpp) REVERT: E 105 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8079 (mt-10) REVERT: F 32 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: F 53 GLU cc_start: 0.8361 (tt0) cc_final: 0.7846 (tt0) REVERT: F 68 ASP cc_start: 0.8140 (m-30) cc_final: 0.7599 (t70) REVERT: F 74 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8317 (mm-30) REVERT: F 79 LYS cc_start: 0.8965 (mttm) cc_final: 0.8428 (tptp) REVERT: F 84 MET cc_start: 0.8103 (mmm) cc_final: 0.7754 (tpp) REVERT: F 88 TYR cc_start: 0.7917 (m-10) cc_final: 0.7536 (m-10) REVERT: F 90 LEU cc_start: 0.8710 (mm) cc_final: 0.8055 (tt) REVERT: F 91 LYS cc_start: 0.8409 (mttt) cc_final: 0.8112 (mtpt) REVERT: G 90 MET cc_start: 0.8837 (mmp) cc_final: 0.8478 (tpt) REVERT: G 120 MET cc_start: 0.8445 (mmm) cc_final: 0.7886 (mmt) REVERT: H 52 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7425 (tm-30) REVERT: H 79 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8603 (ttmm) outliers start: 20 outliers final: 18 residues processed: 182 average time/residue: 0.2494 time to fit residues: 60.2138 Evaluate side-chains 183 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.094708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063589 restraints weight = 31918.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065154 restraints weight = 19307.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066189 restraints weight = 14393.511| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.217 Angle : 0.635 10.747 15097 Z= 0.362 Chirality : 0.034 0.173 1724 Planarity : 0.004 0.032 1074 Dihedral : 31.717 176.999 3290 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.15 % Allowed : 34.78 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.34), residues: 580 helix: 2.93 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -1.69 (0.41), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 75 PHE 0.010 0.001 PHE E 104 TYR 0.009 0.001 TYR D 88 ARG 0.007 0.000 ARG H 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.03 seconds wall clock time: 32 minutes 59.77 seconds (1979.77 seconds total)