Starting phenix.real_space_refine on Thu Mar 14 20:39:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/03_2024/7yoz_33991.pdb" } resolution = 4.3 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 5365 2.51 5 N 1838 2.21 5 O 2287 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 83": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" 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: 9752 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: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} 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: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} 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: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} 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: 5.55, per 1000 atoms: 0.57 Number of scatterers: 9752 At special positions: 0 Unit cell: (122.85, 90.3, 113.4, 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 2287 8.00 N 1838 7.00 C 5365 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: 4.40 Conformation dependent library (CDL) restraints added in 684.2 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 79.1% alpha, 0.7% beta 120 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.614A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.575A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.537A 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 93 removed outlier: 3.512A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.526A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.563A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.537A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.653A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.818A 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 removed outlier: 3.593A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 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 93 Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.722A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 350 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.45: 3358 1.45 - 1.57: 4570 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10403 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB ARG G 128 " pdb=" CG ARG G 128 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.40e-02 5.10e+03 1.37e+00 bond pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CE LYS G 64 " pdb=" NZ LYS G 64 " ideal model delta sigma weight residual 1.489 1.457 0.032 3.00e-02 1.11e+03 1.15e+00 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 99.23 - 105.87: 1262 105.87 - 112.52: 5646 112.52 - 119.16: 2709 119.16 - 125.81: 4655 125.81 - 132.45: 796 Bond angle restraints: 15068 Sorted by residual: angle pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " pdb=" CD1 LEU A 103 " ideal model delta sigma weight residual 110.70 103.05 7.65 3.00e+00 1.11e-01 6.50e+00 angle pdb=" N SER C 86 " pdb=" CA SER C 86 " pdb=" C SER C 86 " ideal model delta sigma weight residual 111.07 113.75 -2.68 1.07e+00 8.73e-01 6.25e+00 angle pdb=" CA LEU B 62 " pdb=" CB LEU B 62 " pdb=" CG LEU B 62 " ideal model delta sigma weight residual 116.30 124.22 -7.92 3.50e+00 8.16e-02 5.12e+00 angle pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " pdb=" NH1 ARG B 92 " ideal model delta sigma weight residual 121.50 119.26 2.24 1.00e+00 1.00e+00 5.00e+00 angle pdb=" C LEU B 90 " pdb=" N LYS B 91 " pdb=" CA LYS B 91 " ideal model delta sigma weight residual 120.28 123.27 -2.99 1.34e+00 5.57e-01 4.97e+00 ... (remaining 15063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4528 35.80 - 71.59: 1090 71.59 - 107.39: 15 107.39 - 143.19: 1 143.19 - 178.98: 3 Dihedral angle restraints: 5637 sinusoidal: 3911 harmonic: 1726 Sorted by residual: 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 -140.00 38.98 -178.98 1 3.50e+01 8.16e-04 1.57e+01 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 36.13 -176.13 1 3.50e+01 8.16e-04 1.57e+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 76.24 143.76 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1559 0.050 - 0.101: 141 0.101 - 0.151: 20 0.151 - 0.201: 1 0.201 - 0.252: 2 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CG LEU A 103 " pdb=" CB LEU A 103 " pdb=" CD1 LEU A 103 " pdb=" CD2 LEU A 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU G 103 " pdb=" CB LEU G 103 " pdb=" CD1 LEU G 103 " pdb=" CD2 LEU G 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA THR G 107 " pdb=" N THR G 107 " pdb=" C THR G 107 " pdb=" CB THR G 107 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1720 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 77 " 0.024 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" CG ASP E 77 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASP E 77 " 0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP E 77 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 31 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO D 32 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.031 9.50e-02 1.11e+02 1.84e-02 1.96e+00 pdb=" NE ARG B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " -0.007 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1872 2.80 - 3.32: 8558 3.32 - 3.85: 18168 3.85 - 4.37: 20847 4.37 - 4.90: 29311 Nonbonded interactions: 78756 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.269 2.520 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.270 2.520 nonbonded pdb=" NZ LYS C 115 " pdb=" OP2 DT J 29 " model vdw 2.324 2.520 nonbonded pdb=" NE ARG G 128 " pdb=" OE1 GLU G 133 " model vdw 2.359 2.520 nonbonded pdb=" NZ LYS G 79 " pdb=" OE1 GLU H 74 " model vdw 2.366 2.520 ... (remaining 78751 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 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } 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: 0.360 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: 1.770 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.090 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.037 10403 Z= 0.171 Angle : 0.552 7.918 15068 Z= 0.361 Chirality : 0.032 0.252 1723 Planarity : 0.004 0.050 1069 Dihedral : 27.407 178.984 4513 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.64 (0.30), residues: 578 helix: 0.94 (0.21), residues: 450 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.014 0.001 PHE G 104 TYR 0.012 0.001 TYR D 88 ARG 0.024 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 0.685 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 64 LYS cc_start: 0.8892 (mttm) cc_final: 0.8550 (mtmm) REVERT: A 68 GLN cc_start: 0.8865 (tt0) cc_final: 0.8408 (tp40) REVERT: A 85 GLN cc_start: 0.8636 (tt0) cc_final: 0.8300 (tp40) REVERT: A 93 GLN cc_start: 0.8676 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 119 ILE cc_start: 0.9037 (pt) cc_final: 0.8346 (mt) REVERT: A 120 MET cc_start: 0.8634 (mmm) cc_final: 0.8410 (mmm) REVERT: A 123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8472 (t70) REVERT: A 126 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp) REVERT: A 128 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8313 (mtp180) REVERT: A 130 ILE cc_start: 0.9707 (mt) cc_final: 0.9487 (mm) REVERT: B 51 TYR cc_start: 0.8033 (m-80) cc_final: 0.7735 (m-80) REVERT: C 104 PHE cc_start: 0.9000 (m-80) cc_final: 0.8537 (m-80) REVERT: C 121 PRO cc_start: 0.8849 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: C 123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8366 (m-30) REVERT: C 124 ILE cc_start: 0.9349 (mt) cc_final: 0.9097 (tp) REVERT: C 130 ILE cc_start: 0.8366 (tt) cc_final: 0.8042 (tt) REVERT: D 43 VAL cc_start: 0.8313 (t) cc_final: 0.7889 (t) REVERT: D 52 GLU cc_start: 0.9122 (tt0) cc_final: 0.8831 (pp20) REVERT: D 55 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8372 (mmm-85) REVERT: D 59 LYS cc_start: 0.9150 (tttt) cc_final: 0.8326 (tptt) REVERT: D 66 ILE cc_start: 0.9140 (mm) cc_final: 0.8911 (pt) REVERT: D 71 THR cc_start: 0.8948 (m) cc_final: 0.8443 (m) REVERT: E 60 LEU cc_start: 0.6207 (mt) cc_final: 0.5995 (mp) REVERT: E 70 LEU cc_start: 0.8786 (tp) cc_final: 0.8246 (tt) REVERT: E 87 SER cc_start: 0.8980 (m) cc_final: 0.8511 (p) REVERT: E 104 PHE cc_start: 0.8998 (m-80) cc_final: 0.8464 (m-80) REVERT: E 109 LEU cc_start: 0.9725 (tp) cc_final: 0.9503 (tp) REVERT: E 126 LEU cc_start: 0.9139 (tp) cc_final: 0.8919 (tt) REVERT: F 59 LYS cc_start: 0.9204 (tttt) cc_final: 0.8908 (ttpt) REVERT: F 66 ILE cc_start: 0.9055 (mm) cc_final: 0.8817 (pt) REVERT: G 70 LEU cc_start: 0.9140 (tp) cc_final: 0.8380 (tt) REVERT: G 90 MET cc_start: 0.8385 (ttm) cc_final: 0.8051 (tmm) REVERT: G 97 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7721 (mt-10) REVERT: G 123 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (t70) REVERT: H 35 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7964 (ttt180) REVERT: H 43 VAL cc_start: 0.6861 (t) cc_final: 0.5771 (t) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3426 time to fit residues: 140.4001 Evaluate side-chains 222 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10403 Z= 0.296 Angle : 0.699 9.213 15068 Z= 0.405 Chirality : 0.038 0.186 1723 Planarity : 0.006 0.054 1069 Dihedral : 31.713 179.250 3286 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.60 % Allowed : 4.56 % Favored : 94.84 % 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: 1.69 (0.33), residues: 578 helix: 1.68 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.025 0.002 PHE A 104 TYR 0.022 0.002 TYR D 72 ARG 0.012 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 0.665 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: A 61 LEU cc_start: 0.8175 (tt) cc_final: 0.7963 (tt) REVERT: A 64 LYS cc_start: 0.9319 (mttm) cc_final: 0.8882 (mtmm) REVERT: A 68 GLN cc_start: 0.8996 (tt0) cc_final: 0.8195 (tt0) REVERT: A 85 GLN cc_start: 0.9142 (tt0) cc_final: 0.8738 (tp40) REVERT: A 92 LEU cc_start: 0.9705 (tt) cc_final: 0.9373 (tt) REVERT: A 93 GLN cc_start: 0.8986 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 96 CYS cc_start: 0.8984 (m) cc_final: 0.8718 (p) REVERT: A 97 GLU cc_start: 0.8147 (tt0) cc_final: 0.7342 (mt-10) REVERT: A 119 ILE cc_start: 0.9238 (pt) cc_final: 0.9005 (mt) REVERT: A 123 ASP cc_start: 0.8691 (m-30) cc_final: 0.8362 (t70) REVERT: A 130 ILE cc_start: 0.9789 (mt) cc_final: 0.9487 (mm) REVERT: B 24 ASP cc_start: 0.8294 (t0) cc_final: 0.7581 (p0) REVERT: B 88 TYR cc_start: 0.8776 (m-80) cc_final: 0.8575 (m-80) REVERT: C 90 MET cc_start: 0.9208 (ppp) cc_final: 0.8772 (ppp) REVERT: C 93 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8890 (tm-30) REVERT: C 94 GLU cc_start: 0.9218 (pt0) cc_final: 0.8900 (pt0) REVERT: C 106 ASP cc_start: 0.9081 (m-30) cc_final: 0.8378 (m-30) REVERT: C 123 ASP cc_start: 0.9221 (m-30) cc_final: 0.8774 (m-30) REVERT: D 49 LEU cc_start: 0.8497 (pp) cc_final: 0.8245 (pt) REVERT: D 52 GLU cc_start: 0.9159 (tt0) cc_final: 0.8913 (pp20) REVERT: D 55 ARG cc_start: 0.9051 (mtt180) cc_final: 0.8546 (mmm-85) REVERT: D 59 LYS cc_start: 0.9199 (tttt) cc_final: 0.8470 (tptp) REVERT: D 63 GLU cc_start: 0.8926 (tt0) cc_final: 0.8492 (tm-30) REVERT: E 87 SER cc_start: 0.8938 (m) cc_final: 0.8488 (p) REVERT: E 119 ILE cc_start: 0.8189 (pt) cc_final: 0.7763 (pt) REVERT: E 120 MET cc_start: 0.8726 (mmp) cc_final: 0.8297 (mmm) REVERT: E 123 ASP cc_start: 0.8982 (m-30) cc_final: 0.8687 (m-30) REVERT: F 36 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8600 (ttp80) REVERT: F 49 LEU cc_start: 0.9280 (tt) cc_final: 0.8616 (tt) REVERT: F 50 ILE cc_start: 0.9460 (tp) cc_final: 0.9237 (mm) REVERT: F 59 LYS cc_start: 0.9271 (tttt) cc_final: 0.9004 (ttmt) REVERT: F 60 VAL cc_start: 0.9147 (p) cc_final: 0.8246 (p) REVERT: F 81 VAL cc_start: 0.6099 (t) cc_final: 0.5870 (t) REVERT: F 82 THR cc_start: 0.6035 (p) cc_final: 0.5516 (p) REVERT: G 68 GLN cc_start: 0.9180 (tm130) cc_final: 0.8286 (tm-30) REVERT: G 90 MET cc_start: 0.8636 (ttm) cc_final: 0.8111 (tmm) REVERT: G 96 CYS cc_start: 0.8202 (m) cc_final: 0.7871 (m) REVERT: G 123 ASP cc_start: 0.8581 (m-30) cc_final: 0.8379 (t70) REVERT: G 126 LEU cc_start: 0.9658 (tp) cc_final: 0.9393 (tt) REVERT: G 128 ARG cc_start: 0.9032 (mtp-110) cc_final: 0.8752 (mtp-110) REVERT: H 35 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8381 (ttt90) REVERT: H 74 GLU cc_start: 0.9093 (tt0) cc_final: 0.8587 (tt0) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.2961 time to fit residues: 99.0175 Evaluate side-chains 213 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10403 Z= 0.255 Angle : 0.641 8.066 15068 Z= 0.370 Chirality : 0.034 0.173 1723 Planarity : 0.005 0.044 1069 Dihedral : 31.543 179.600 3286 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: 1.88 (0.34), residues: 578 helix: 1.80 (0.24), residues: 467 sheet: None (None), residues: 0 loop : -1.14 (0.48), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.014 0.002 PHE G 104 TYR 0.010 0.001 TYR D 72 ARG 0.007 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.764 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: A 64 LYS cc_start: 0.9366 (mttm) cc_final: 0.9067 (mtmm) REVERT: A 85 GLN cc_start: 0.9029 (tt0) cc_final: 0.8806 (mm110) REVERT: A 97 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 120 MET cc_start: 0.8913 (mmm) cc_final: 0.8663 (mmm) REVERT: B 24 ASP cc_start: 0.8438 (t0) cc_final: 0.8106 (t0) REVERT: B 35 ARG cc_start: 0.8158 (ttt90) cc_final: 0.7241 (ttt90) REVERT: B 39 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7755 (mtm-85) REVERT: B 85 ASP cc_start: 0.9160 (m-30) cc_final: 0.8934 (m-30) REVERT: C 90 MET cc_start: 0.9144 (ppp) cc_final: 0.8690 (ppp) REVERT: C 93 GLN cc_start: 0.9177 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 123 ASP cc_start: 0.9202 (m-30) cc_final: 0.8831 (m-30) REVERT: D 49 LEU cc_start: 0.8393 (pp) cc_final: 0.8164 (pt) REVERT: D 63 GLU cc_start: 0.9042 (tt0) cc_final: 0.8581 (tm-30) REVERT: D 66 ILE cc_start: 0.9222 (mt) cc_final: 0.8914 (pt) REVERT: E 70 LEU cc_start: 0.9096 (tp) cc_final: 0.8429 (mt) REVERT: E 76 GLN cc_start: 0.8873 (tt0) cc_final: 0.8355 (tp-100) REVERT: E 87 SER cc_start: 0.8812 (m) cc_final: 0.8600 (p) REVERT: E 90 MET cc_start: 0.8575 (ppp) cc_final: 0.8034 (ppp) REVERT: E 93 GLN cc_start: 0.9231 (mm110) cc_final: 0.8642 (tp40) REVERT: E 94 GLU cc_start: 0.8757 (pt0) cc_final: 0.7938 (pt0) REVERT: E 119 ILE cc_start: 0.8584 (pt) cc_final: 0.8239 (pt) REVERT: E 120 MET cc_start: 0.8537 (mmp) cc_final: 0.8207 (mmm) REVERT: F 36 ARG cc_start: 0.8862 (mtm110) cc_final: 0.8606 (ttp80) REVERT: F 55 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8288 (mmm-85) REVERT: F 60 VAL cc_start: 0.9054 (p) cc_final: 0.8517 (p) REVERT: F 63 GLU cc_start: 0.9276 (pt0) cc_final: 0.9005 (pp20) REVERT: F 82 THR cc_start: 0.7095 (p) cc_final: 0.6859 (p) REVERT: F 84 MET cc_start: 0.8774 (ptt) cc_final: 0.8507 (ptt) REVERT: F 88 TYR cc_start: 0.9035 (m-80) cc_final: 0.8782 (t80) REVERT: G 90 MET cc_start: 0.8780 (ttm) cc_final: 0.8203 (tmm) REVERT: G 96 CYS cc_start: 0.8664 (m) cc_final: 0.8405 (m) REVERT: G 128 ARG cc_start: 0.9054 (mtp-110) cc_final: 0.8600 (mtp-110) REVERT: H 35 ARG cc_start: 0.8909 (mtp85) cc_final: 0.8138 (ttm110) REVERT: H 74 GLU cc_start: 0.9108 (tt0) cc_final: 0.8890 (tt0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2918 time to fit residues: 99.7015 Evaluate side-chains 223 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10403 Z= 0.193 Angle : 0.599 7.665 15068 Z= 0.350 Chirality : 0.033 0.141 1723 Planarity : 0.004 0.032 1069 Dihedral : 31.532 179.787 3286 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 1.95 (0.33), residues: 578 helix: 1.89 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 113 PHE 0.009 0.001 PHE A 104 TYR 0.018 0.001 TYR F 72 ARG 0.007 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 0.756 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 64 LYS cc_start: 0.9379 (mttm) cc_final: 0.9065 (mtmm) REVERT: A 68 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 85 GLN cc_start: 0.8972 (tt0) cc_final: 0.8535 (mm-40) REVERT: A 86 SER cc_start: 0.8699 (m) cc_final: 0.8418 (m) REVERT: B 24 ASP cc_start: 0.8440 (t0) cc_final: 0.7401 (p0) REVERT: B 65 VAL cc_start: 0.9444 (t) cc_final: 0.9146 (p) REVERT: C 90 MET cc_start: 0.9103 (ppp) cc_final: 0.8632 (ppp) REVERT: C 93 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 123 ASP cc_start: 0.9125 (m-30) cc_final: 0.8854 (m-30) REVERT: D 27 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8764 (mp10) REVERT: D 49 LEU cc_start: 0.8086 (pp) cc_final: 0.7853 (pt) REVERT: D 52 GLU cc_start: 0.8673 (pp20) cc_final: 0.8431 (pp20) REVERT: D 55 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8567 (mmm-85) REVERT: D 63 GLU cc_start: 0.8959 (tt0) cc_final: 0.8516 (tm-30) REVERT: D 66 ILE cc_start: 0.9081 (mt) cc_final: 0.8817 (pt) REVERT: E 70 LEU cc_start: 0.9157 (tp) cc_final: 0.8503 (mt) REVERT: E 76 GLN cc_start: 0.8793 (tt0) cc_final: 0.8273 (tp-100) REVERT: E 90 MET cc_start: 0.8490 (ppp) cc_final: 0.7965 (ppp) REVERT: E 93 GLN cc_start: 0.9193 (mm110) cc_final: 0.8909 (mm110) REVERT: E 94 GLU cc_start: 0.8739 (pt0) cc_final: 0.7958 (pt0) REVERT: E 110 CYS cc_start: 0.8687 (t) cc_final: 0.7976 (t) REVERT: E 119 ILE cc_start: 0.8305 (pt) cc_final: 0.7953 (pt) REVERT: E 123 ASP cc_start: 0.8675 (m-30) cc_final: 0.8097 (m-30) REVERT: E 128 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: F 49 LEU cc_start: 0.9269 (tt) cc_final: 0.8574 (tt) REVERT: F 55 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8381 (mmm-85) REVERT: F 60 VAL cc_start: 0.9123 (p) cc_final: 0.8717 (p) REVERT: F 63 GLU cc_start: 0.9293 (pt0) cc_final: 0.9019 (pp20) REVERT: F 82 THR cc_start: 0.7433 (p) cc_final: 0.7197 (p) REVERT: F 90 LEU cc_start: 0.8878 (tt) cc_final: 0.8544 (pp) REVERT: G 60 LEU cc_start: 0.8120 (mm) cc_final: 0.7809 (mm) REVERT: G 90 MET cc_start: 0.8692 (ttm) cc_final: 0.8266 (tmm) REVERT: G 93 GLN cc_start: 0.8594 (pt0) cc_final: 0.8081 (pt0) REVERT: G 97 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6566 (mt-10) REVERT: G 120 MET cc_start: 0.9353 (mmm) cc_final: 0.9050 (mmm) REVERT: G 123 ASP cc_start: 0.8480 (t70) cc_final: 0.8219 (t70) REVERT: G 128 ARG cc_start: 0.8881 (mtp-110) cc_final: 0.8011 (mtp-110) REVERT: H 74 GLU cc_start: 0.9026 (tt0) cc_final: 0.8704 (tt0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2847 time to fit residues: 100.4640 Evaluate side-chains 232 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.9182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10403 Z= 0.282 Angle : 0.667 5.907 15068 Z= 0.392 Chirality : 0.037 0.179 1723 Planarity : 0.005 0.044 1069 Dihedral : 32.222 178.813 3286 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.20 % Allowed : 5.95 % Favored : 93.85 % 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: 1.29 (0.32), residues: 578 helix: 1.43 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 75 PHE 0.025 0.002 PHE G 104 TYR 0.011 0.002 TYR B 88 ARG 0.014 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 0.781 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 60 LEU cc_start: 0.9068 (mm) cc_final: 0.8758 (mt) REVERT: A 61 LEU cc_start: 0.9090 (tt) cc_final: 0.8850 (tt) REVERT: A 68 GLN cc_start: 0.9400 (tm-30) cc_final: 0.8961 (tm-30) REVERT: A 72 ARG cc_start: 0.8409 (mmm160) cc_final: 0.8056 (mmt-90) REVERT: A 96 CYS cc_start: 0.8907 (m) cc_final: 0.8689 (m) REVERT: A 97 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 115 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8733 (mmmm) REVERT: B 63 GLU cc_start: 0.8690 (tt0) cc_final: 0.8165 (tp30) REVERT: B 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.9001 (m-30) REVERT: C 78 PHE cc_start: 0.8509 (t80) cc_final: 0.8174 (t80) REVERT: C 90 MET cc_start: 0.9037 (ppp) cc_final: 0.8445 (ppp) REVERT: C 93 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 97 GLU cc_start: 0.9071 (tt0) cc_final: 0.8790 (tt0) REVERT: D 27 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8859 (mp10) REVERT: D 44 LYS cc_start: 0.9007 (mttp) cc_final: 0.8337 (mtpp) REVERT: D 55 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8474 (mmm-85) REVERT: D 63 GLU cc_start: 0.9165 (tt0) cc_final: 0.8857 (tm-30) REVERT: D 66 ILE cc_start: 0.9300 (mt) cc_final: 0.9041 (pt) REVERT: E 76 GLN cc_start: 0.8851 (tt0) cc_final: 0.8278 (tp-100) REVERT: E 93 GLN cc_start: 0.9233 (mm110) cc_final: 0.9030 (mm110) REVERT: E 119 ILE cc_start: 0.8512 (pt) cc_final: 0.8286 (pt) REVERT: E 120 MET cc_start: 0.8562 (mmm) cc_final: 0.8137 (mmm) REVERT: F 49 LEU cc_start: 0.9138 (tt) cc_final: 0.7834 (tp) REVERT: F 54 THR cc_start: 0.8951 (p) cc_final: 0.8638 (p) REVERT: F 60 VAL cc_start: 0.9185 (p) cc_final: 0.8661 (p) REVERT: F 63 GLU cc_start: 0.9380 (pt0) cc_final: 0.9111 (pp20) REVERT: G 60 LEU cc_start: 0.8449 (mm) cc_final: 0.8206 (mt) REVERT: G 97 GLU cc_start: 0.7906 (mt-10) cc_final: 0.6927 (mt-10) REVERT: G 106 ASP cc_start: 0.9083 (t70) cc_final: 0.8851 (t70) REVERT: G 123 ASP cc_start: 0.8355 (t70) cc_final: 0.8010 (t70) REVERT: G 128 ARG cc_start: 0.8844 (mtp-110) cc_final: 0.8125 (mtp-110) REVERT: H 63 GLU cc_start: 0.8432 (tt0) cc_final: 0.8093 (tt0) REVERT: H 65 VAL cc_start: 0.9541 (t) cc_final: 0.9312 (p) REVERT: H 67 ARG cc_start: 0.9157 (ttm170) cc_final: 0.8786 (ttm170) REVERT: H 74 GLU cc_start: 0.9091 (tt0) cc_final: 0.8845 (tt0) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.2911 time to fit residues: 104.1987 Evaluate side-chains 239 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8215 moved from start: 1.0009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10403 Z= 0.265 Angle : 0.652 7.428 15068 Z= 0.385 Chirality : 0.036 0.177 1723 Planarity : 0.004 0.038 1069 Dihedral : 32.250 179.759 3286 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: 1.09 (0.33), residues: 578 helix: 1.26 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 113 PHE 0.021 0.002 PHE G 104 TYR 0.010 0.002 TYR H 51 ARG 0.011 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 0.727 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 64 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8783 (mtmm) REVERT: A 72 ARG cc_start: 0.8401 (mmm160) cc_final: 0.8054 (mmt180) REVERT: A 90 MET cc_start: 0.8158 (tmm) cc_final: 0.7882 (tmm) REVERT: A 115 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8731 (mmmm) REVERT: A 123 ASP cc_start: 0.8634 (m-30) cc_final: 0.8393 (m-30) REVERT: B 63 GLU cc_start: 0.8677 (tt0) cc_final: 0.8216 (tp30) REVERT: B 67 ARG cc_start: 0.9093 (ttm170) cc_final: 0.8838 (ttm-80) REVERT: C 65 LEU cc_start: 0.9351 (tp) cc_final: 0.9066 (tp) REVERT: C 69 ARG cc_start: 0.9300 (mtm180) cc_final: 0.9031 (mtm180) REVERT: C 90 MET cc_start: 0.8990 (ppp) cc_final: 0.8569 (ppp) REVERT: C 97 GLU cc_start: 0.9046 (tt0) cc_final: 0.8634 (tp30) REVERT: C 123 ASP cc_start: 0.9303 (m-30) cc_final: 0.9084 (m-30) REVERT: D 44 LYS cc_start: 0.9084 (mttp) cc_final: 0.8407 (mtpp) REVERT: D 63 GLU cc_start: 0.9223 (tt0) cc_final: 0.8899 (tm-30) REVERT: D 66 ILE cc_start: 0.9385 (mt) cc_final: 0.9139 (pt) REVERT: D 84 MET cc_start: 0.8991 (mmm) cc_final: 0.8534 (ppp) REVERT: E 76 GLN cc_start: 0.9002 (tt0) cc_final: 0.8397 (tp-100) REVERT: E 119 ILE cc_start: 0.8636 (pt) cc_final: 0.8320 (pt) REVERT: E 120 MET cc_start: 0.8550 (mmm) cc_final: 0.8107 (mmm) REVERT: F 29 ILE cc_start: 0.9512 (mm) cc_final: 0.9131 (mm) REVERT: F 60 VAL cc_start: 0.9136 (p) cc_final: 0.8493 (p) REVERT: F 63 GLU cc_start: 0.9387 (pt0) cc_final: 0.9109 (pp20) REVERT: F 66 ILE cc_start: 0.9485 (mt) cc_final: 0.9269 (pt) REVERT: F 78 ARG cc_start: 0.7190 (ptm160) cc_final: 0.6869 (ptm-80) REVERT: F 82 THR cc_start: 0.7909 (p) cc_final: 0.7465 (p) REVERT: G 61 LEU cc_start: 0.9049 (tt) cc_final: 0.8444 (tt) REVERT: G 68 GLN cc_start: 0.9064 (pp30) cc_final: 0.8763 (pp30) REVERT: G 97 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6908 (mt-10) REVERT: G 116 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8423 (mtm180) REVERT: G 120 MET cc_start: 0.9202 (mmm) cc_final: 0.8688 (mmm) REVERT: G 128 ARG cc_start: 0.8737 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: H 39 ARG cc_start: 0.8854 (mpt-90) cc_final: 0.8562 (mmm160) REVERT: H 65 VAL cc_start: 0.9551 (t) cc_final: 0.9321 (p) REVERT: H 74 GLU cc_start: 0.9086 (tt0) cc_final: 0.8801 (tt0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2946 time to fit residues: 102.6122 Evaluate side-chains 233 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 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: 7.9990 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 1.0111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10403 Z= 0.213 Angle : 0.649 13.195 15068 Z= 0.369 Chirality : 0.035 0.181 1723 Planarity : 0.004 0.068 1069 Dihedral : 31.945 179.726 3286 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.06 (0.33), residues: 578 helix: 1.23 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.018 0.002 PHE A 104 TYR 0.015 0.001 TYR D 72 ARG 0.015 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.732 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 64 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8613 (mtmt) REVERT: A 90 MET cc_start: 0.7893 (tmm) cc_final: 0.7664 (tmm) REVERT: A 106 ASP cc_start: 0.9138 (t70) cc_final: 0.8888 (t70) REVERT: A 123 ASP cc_start: 0.8617 (m-30) cc_final: 0.8405 (m-30) REVERT: B 67 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8768 (ttm-80) REVERT: C 78 PHE cc_start: 0.8603 (t80) cc_final: 0.8396 (t80) REVERT: C 87 SER cc_start: 0.8756 (p) cc_final: 0.8476 (p) REVERT: C 90 MET cc_start: 0.9047 (ppp) cc_final: 0.8529 (ppp) REVERT: C 93 GLN cc_start: 0.8725 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 97 GLU cc_start: 0.9009 (tt0) cc_final: 0.8619 (tt0) REVERT: D 44 LYS cc_start: 0.8951 (mttp) cc_final: 0.8423 (mtpp) REVERT: D 63 GLU cc_start: 0.9191 (tt0) cc_final: 0.8714 (tm-30) REVERT: D 66 ILE cc_start: 0.9452 (mt) cc_final: 0.9239 (pt) REVERT: E 64 LYS cc_start: 0.8783 (mmpt) cc_final: 0.7967 (mmmt) REVERT: E 68 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8514 (tp-100) REVERT: E 76 GLN cc_start: 0.9002 (tt0) cc_final: 0.8433 (tp-100) REVERT: E 119 ILE cc_start: 0.8521 (pt) cc_final: 0.8204 (pt) REVERT: E 120 MET cc_start: 0.8424 (mmm) cc_final: 0.7887 (mmm) REVERT: F 55 ARG cc_start: 0.9139 (mtt90) cc_final: 0.8339 (mmm-85) REVERT: F 60 VAL cc_start: 0.9131 (p) cc_final: 0.8470 (p) REVERT: F 63 GLU cc_start: 0.9399 (pt0) cc_final: 0.9052 (pp20) REVERT: F 66 ILE cc_start: 0.9455 (mt) cc_final: 0.9249 (pt) REVERT: F 78 ARG cc_start: 0.7168 (ptm160) cc_final: 0.6965 (ptm160) REVERT: F 82 THR cc_start: 0.8051 (p) cc_final: 0.7742 (t) REVERT: G 61 LEU cc_start: 0.9059 (tt) cc_final: 0.8539 (tt) REVERT: G 93 GLN cc_start: 0.8928 (pt0) cc_final: 0.8088 (pt0) REVERT: G 97 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6593 (mt-10) REVERT: G 116 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8021 (mtm180) REVERT: G 120 MET cc_start: 0.9199 (mmm) cc_final: 0.8535 (mmm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2875 time to fit residues: 99.0347 Evaluate side-chains 235 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 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: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 1.0355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10403 Z= 0.223 Angle : 0.646 7.821 15068 Z= 0.371 Chirality : 0.035 0.182 1723 Planarity : 0.005 0.061 1069 Dihedral : 31.993 179.096 3286 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 1.06 (0.34), residues: 578 helix: 1.22 (0.24), residues: 467 sheet: None (None), residues: 0 loop : -1.40 (0.48), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.020 0.002 PHE G 104 TYR 0.021 0.001 TYR B 88 ARG 0.012 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 0.678 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: A 83 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7666 (mtp-110) REVERT: A 123 ASP cc_start: 0.8600 (m-30) cc_final: 0.8386 (m-30) REVERT: C 78 PHE cc_start: 0.8618 (t80) cc_final: 0.8380 (t80) REVERT: C 87 SER cc_start: 0.8745 (p) cc_final: 0.8478 (p) REVERT: C 90 MET cc_start: 0.9017 (ppp) cc_final: 0.8417 (ppp) REVERT: C 94 GLU cc_start: 0.9176 (pt0) cc_final: 0.8883 (pp20) REVERT: C 123 ASP cc_start: 0.9242 (m-30) cc_final: 0.9042 (m-30) REVERT: D 29 ILE cc_start: 0.9051 (mm) cc_final: 0.8799 (mm) REVERT: D 44 LYS cc_start: 0.9007 (mttp) cc_final: 0.8512 (mtpp) REVERT: D 55 ARG cc_start: 0.9095 (mtt180) cc_final: 0.8664 (mtt90) REVERT: D 63 GLU cc_start: 0.9179 (tt0) cc_final: 0.8705 (tm-30) REVERT: D 66 ILE cc_start: 0.9459 (mt) cc_final: 0.9235 (pt) REVERT: D 84 MET cc_start: 0.8914 (mmm) cc_final: 0.8584 (ppp) REVERT: E 76 GLN cc_start: 0.8994 (tt0) cc_final: 0.8394 (tp-100) REVERT: E 110 CYS cc_start: 0.8308 (t) cc_final: 0.7740 (t) REVERT: E 119 ILE cc_start: 0.8573 (pt) cc_final: 0.8318 (pt) REVERT: E 123 ASP cc_start: 0.8623 (m-30) cc_final: 0.8235 (m-30) REVERT: F 49 LEU cc_start: 0.9137 (tt) cc_final: 0.8926 (tp) REVERT: F 53 GLU cc_start: 0.9172 (pt0) cc_final: 0.8767 (pt0) REVERT: F 60 VAL cc_start: 0.9114 (p) cc_final: 0.8432 (p) REVERT: F 63 GLU cc_start: 0.9402 (pt0) cc_final: 0.9042 (pp20) REVERT: F 66 ILE cc_start: 0.9468 (mt) cc_final: 0.9256 (pt) REVERT: F 78 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6739 (ptm-80) REVERT: F 82 THR cc_start: 0.8084 (p) cc_final: 0.7638 (p) REVERT: G 68 GLN cc_start: 0.8986 (pp30) cc_final: 0.8719 (pp30) REVERT: G 93 GLN cc_start: 0.8816 (pt0) cc_final: 0.7654 (tm-30) REVERT: H 92 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8168 (ttp80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2693 time to fit residues: 89.1689 Evaluate side-chains 228 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 1.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10403 Z= 0.318 Angle : 0.729 8.414 15068 Z= 0.420 Chirality : 0.039 0.205 1723 Planarity : 0.005 0.082 1069 Dihedral : 32.703 178.589 3286 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.76 (0.33), residues: 578 helix: 1.03 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -1.51 (0.49), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 113 PHE 0.029 0.002 PHE G 104 TYR 0.023 0.003 TYR B 88 ARG 0.014 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.731 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 61 LEU cc_start: 0.8783 (tt) cc_final: 0.8578 (tt) REVERT: A 64 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8770 (pttt) REVERT: A 68 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8924 (tm-30) REVERT: A 93 GLN cc_start: 0.8295 (tp40) cc_final: 0.7937 (tp40) REVERT: A 115 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8813 (mmmm) REVERT: A 123 ASP cc_start: 0.8753 (m-30) cc_final: 0.8254 (m-30) REVERT: B 27 GLN cc_start: 0.8954 (mm110) cc_final: 0.8665 (mm110) REVERT: B 63 GLU cc_start: 0.8705 (tt0) cc_final: 0.8201 (tp30) REVERT: B 74 GLU cc_start: 0.8174 (pp20) cc_final: 0.7905 (pp20) REVERT: B 85 ASP cc_start: 0.9190 (m-30) cc_final: 0.8971 (m-30) REVERT: C 78 PHE cc_start: 0.8633 (t80) cc_final: 0.8322 (t80) REVERT: C 94 GLU cc_start: 0.9231 (pt0) cc_final: 0.8945 (pp20) REVERT: C 106 ASP cc_start: 0.8297 (m-30) cc_final: 0.8022 (m-30) REVERT: D 44 LYS cc_start: 0.9060 (mttp) cc_final: 0.8583 (mtpp) REVERT: D 55 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8490 (mtp85) REVERT: D 59 LYS cc_start: 0.9409 (tttt) cc_final: 0.8528 (tptp) REVERT: D 63 GLU cc_start: 0.9235 (tt0) cc_final: 0.8815 (tm-30) REVERT: D 66 ILE cc_start: 0.9585 (mt) cc_final: 0.9384 (pt) REVERT: D 84 MET cc_start: 0.8849 (mmm) cc_final: 0.8569 (ppp) REVERT: E 76 GLN cc_start: 0.9016 (tt0) cc_final: 0.8465 (tp-100) REVERT: E 93 GLN cc_start: 0.9329 (mm110) cc_final: 0.8921 (mm-40) REVERT: E 123 ASP cc_start: 0.8905 (m-30) cc_final: 0.8646 (m-30) REVERT: F 29 ILE cc_start: 0.9568 (mm) cc_final: 0.9218 (mm) REVERT: F 53 GLU cc_start: 0.9170 (pt0) cc_final: 0.8865 (pt0) REVERT: F 60 VAL cc_start: 0.9033 (p) cc_final: 0.8319 (p) REVERT: F 63 GLU cc_start: 0.9434 (pt0) cc_final: 0.9113 (pp20) REVERT: F 78 ARG cc_start: 0.7374 (ptm160) cc_final: 0.7109 (ptm160) REVERT: F 82 THR cc_start: 0.8064 (p) cc_final: 0.7510 (p) REVERT: G 61 LEU cc_start: 0.9251 (tt) cc_final: 0.8874 (tt) REVERT: G 68 GLN cc_start: 0.9182 (pp30) cc_final: 0.8836 (pp30) REVERT: G 73 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8498 (tm-30) REVERT: G 80 THR cc_start: 0.8540 (p) cc_final: 0.8010 (p) REVERT: G 93 GLN cc_start: 0.9015 (pt0) cc_final: 0.7994 (pt0) REVERT: G 97 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7597 (mt-10) REVERT: G 120 MET cc_start: 0.8836 (mmp) cc_final: 0.8597 (mmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2581 time to fit residues: 88.3579 Evaluate side-chains 229 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 1.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10403 Z= 0.297 Angle : 0.709 8.295 15068 Z= 0.407 Chirality : 0.038 0.197 1723 Planarity : 0.005 0.067 1069 Dihedral : 32.714 179.266 3286 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.74 (0.33), residues: 578 helix: 1.00 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -1.55 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.023 0.002 PHE G 104 TYR 0.021 0.002 TYR B 72 ARG 0.013 0.001 ARG H 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 0.710 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: A 64 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8838 (mtmm) REVERT: A 65 LEU cc_start: 0.9625 (tp) cc_final: 0.9390 (tp) REVERT: A 115 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8864 (mmmm) REVERT: A 123 ASP cc_start: 0.8683 (m-30) cc_final: 0.8166 (m-30) REVERT: C 93 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 94 GLU cc_start: 0.9215 (pt0) cc_final: 0.8972 (pp20) REVERT: C 123 ASP cc_start: 0.9179 (m-30) cc_final: 0.8888 (m-30) REVERT: D 27 GLN cc_start: 0.9069 (mp10) cc_final: 0.8805 (mp10) REVERT: D 44 LYS cc_start: 0.9108 (mttp) cc_final: 0.8633 (mtpp) REVERT: D 54 THR cc_start: 0.9266 (p) cc_final: 0.8939 (p) REVERT: D 55 ARG cc_start: 0.9070 (mtt180) cc_final: 0.8423 (mtt90) REVERT: D 63 GLU cc_start: 0.9294 (tt0) cc_final: 0.8946 (tm-30) REVERT: E 76 GLN cc_start: 0.9042 (tt0) cc_final: 0.8541 (tp-100) REVERT: E 93 GLN cc_start: 0.9306 (mm110) cc_final: 0.9014 (mm110) REVERT: E 110 CYS cc_start: 0.8845 (t) cc_final: 0.8225 (t) REVERT: F 29 ILE cc_start: 0.9578 (mm) cc_final: 0.9371 (mm) REVERT: F 53 GLU cc_start: 0.9259 (pt0) cc_final: 0.8963 (pt0) REVERT: F 60 VAL cc_start: 0.9070 (p) cc_final: 0.8293 (p) REVERT: F 64 ASN cc_start: 0.9247 (t0) cc_final: 0.8990 (m-40) REVERT: F 78 ARG cc_start: 0.7516 (ptm160) cc_final: 0.7308 (ptm160) REVERT: F 82 THR cc_start: 0.8164 (p) cc_final: 0.7731 (p) REVERT: G 61 LEU cc_start: 0.9270 (tt) cc_final: 0.8952 (tt) REVERT: G 68 GLN cc_start: 0.9085 (pp30) cc_final: 0.8746 (pp30) REVERT: G 80 THR cc_start: 0.8498 (p) cc_final: 0.7995 (p) REVERT: G 93 GLN cc_start: 0.8781 (pt0) cc_final: 0.8110 (pt0) REVERT: G 94 GLU cc_start: 0.8875 (pt0) cc_final: 0.8613 (pt0) REVERT: G 97 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7583 (mt-10) REVERT: H 64 ASN cc_start: 0.9222 (m-40) cc_final: 0.8940 (t0) REVERT: H 84 MET cc_start: 0.8808 (ttm) cc_final: 0.8608 (ttm) REVERT: H 92 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8123 (ttp80) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2613 time to fit residues: 89.1644 Evaluate side-chains 231 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 75 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048391 restraints weight = 57302.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049706 restraints weight = 33670.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050610 restraints weight = 23413.719| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 1.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10403 Z= 0.232 Angle : 0.686 8.029 15068 Z= 0.389 Chirality : 0.037 0.176 1723 Planarity : 0.005 0.059 1069 Dihedral : 32.469 179.347 3286 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % 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: 0.76 (0.34), residues: 578 helix: 1.06 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -1.64 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS D 75 PHE 0.023 0.002 PHE G 104 TYR 0.013 0.002 TYR B 72 ARG 0.012 0.001 ARG H 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.67 seconds wall clock time: 38 minutes 51.49 seconds (2331.49 seconds total)