Starting phenix.real_space_refine on Fri Mar 15 13:20:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfc_33171/03_2024/7xfc_33171_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.009 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 285 5.49 5 S 12 5.16 5 C 6521 2.51 5 N 2214 2.21 5 O 2768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 85": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11800 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2911 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 6.62, per 1000 atoms: 0.56 Number of scatterers: 11800 At special positions: 0 Unit cell: (99.94, 115.72, 124.136, 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 12 16.00 P 285 15.00 O 2768 8.00 N 2214 7.00 C 6521 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: 5.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 0 sheets defined 63.9% alpha, 0.0% beta 135 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.900A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.649A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.300A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.011A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.333A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 339 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for ID residue Warning, Cannot make NA restraints for ID residue Restraints generated for nucleic acids: 347 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2233 1.33 - 1.45: 4206 1.45 - 1.57: 5562 1.57 - 1.69: 569 1.69 - 1.81: 22 Bond restraints: 12592 Sorted by residual: bond pdb=" C3' DI I -30 " pdb=" C4' DI I -30 " ideal model delta sigma weight residual 1.315 1.522 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4' DI I -30 " pdb=" O4' DI I -30 " ideal model delta sigma weight residual 1.640 1.435 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C4 DI I -30 " pdb=" N3 DI I -30 " ideal model delta sigma weight residual 1.507 1.354 0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C2 DI I -30 " pdb=" N3 DI I -30 " ideal model delta sigma weight residual 1.482 1.344 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C1' DI I -30 " pdb=" O4' DI I -30 " ideal model delta sigma weight residual 1.311 1.429 -0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 12587 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.97: 1213 104.97 - 112.82: 7209 112.82 - 120.67: 5762 120.67 - 128.52: 3803 128.52 - 136.37: 247 Bond angle restraints: 18234 Sorted by residual: angle pdb=" C1' DI I -30 " pdb=" N9 DI I -30 " pdb=" C4 DI I -30 " ideal model delta sigma weight residual 107.36 124.98 -17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" N GLU H 110 " pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " ideal model delta sigma weight residual 110.28 117.88 -7.60 1.55e+00 4.16e-01 2.40e+01 angle pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 114.10 122.50 -8.40 2.00e+00 2.50e-01 1.76e+01 angle pdb=" C1' DI I -30 " pdb=" N9 DI I -30 " pdb=" C8 DI I -30 " ideal model delta sigma weight residual 138.51 126.75 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " pdb=" CD GLU H 110 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.70e+00 3.46e-01 1.53e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 5437 35.51 - 71.02: 1375 71.02 - 106.54: 12 106.54 - 142.05: 3 142.05 - 177.56: 1 Dihedral angle restraints: 6828 sinusoidal: 4656 harmonic: 2172 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.56 -177.56 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 6825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1560 0.047 - 0.093: 420 0.093 - 0.140: 80 0.140 - 0.187: 13 0.187 - 0.233: 2 Chirality restraints: 2075 Sorted by residual: chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA GLU H 110 " pdb=" N GLU H 110 " pdb=" C GLU H 110 " pdb=" CB GLU H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2072 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO A 121 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO C 80 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO G 80 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.034 5.00e-02 4.00e+02 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 3281 2.85 - 3.36: 9472 3.36 - 3.87: 23804 3.87 - 4.39: 27557 4.39 - 4.90: 38656 Nonbonded interactions: 102770 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.333 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.382 2.440 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.387 2.520 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.398 2.440 nonbonded pdb=" O VAL F 60 " pdb=" ND2 ASN F 64 " model vdw 2.426 2.520 ... (remaining 102765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = (chain 'E' and resid 39 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.010 Extract box with map and model: 2.400 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 38.650 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.007 0.207 12592 Z= 0.341 Angle : 0.774 17.620 18234 Z= 0.446 Chirality : 0.044 0.233 2075 Planarity : 0.007 0.074 1319 Dihedral : 27.752 177.559 5428 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.88 (0.26), residues: 734 helix: -0.38 (0.19), residues: 536 sheet: None (None), residues: 0 loop : -0.71 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.032 0.003 PHE G 25 TYR 0.041 0.002 TYR F 88 ARG 0.018 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.833 Fit side-chains REVERT: A 50 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 79 LYS cc_start: 0.7736 (tttm) cc_final: 0.7484 (ttmt) REVERT: A 105 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 129 ARG cc_start: 0.7157 (tpt90) cc_final: 0.6852 (tpt-90) REVERT: A 133 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7278 (mt-10) REVERT: B 79 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7801 (mmtt) REVERT: D 44 GLN cc_start: 0.7881 (tt0) cc_final: 0.7540 (tt0) REVERT: D 56 MET cc_start: 0.8245 (tpp) cc_final: 0.8005 (tpp) REVERT: D 79 HIS cc_start: 0.7591 (m170) cc_final: 0.7136 (t70) REVERT: D 83 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7642 (mmt90) REVERT: D 96 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7466 (mtm110) REVERT: E 105 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7539 (mt-10) REVERT: F 44 LYS cc_start: 0.8349 (tttt) cc_final: 0.8122 (tttm) REVERT: F 53 GLU cc_start: 0.7057 (tp30) cc_final: 0.6801 (tp30) REVERT: F 91 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8058 (ttmm) REVERT: G 61 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7573 (mm-30) REVERT: G 95 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7619 (tmtt) REVERT: G 99 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6973 (mmm-85) REVERT: H 83 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.7484 (mmt90) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 1.9957 time to fit residues: 380.9622 Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 73 ASN D 106 HIS E 68 GLN E 108 ASN E 113 HIS G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12592 Z= 0.211 Angle : 0.558 6.262 18234 Z= 0.336 Chirality : 0.035 0.153 2075 Planarity : 0.005 0.057 1319 Dihedral : 30.756 178.525 3954 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.25 % Allowed : 11.41 % Favored : 86.33 % 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: 0.88 (0.29), residues: 734 helix: 1.05 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.020 0.002 PHE G 25 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.875 Fit side-chains REVERT: A 50 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 59 GLU cc_start: 0.7850 (pm20) cc_final: 0.7647 (pm20) REVERT: A 105 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 120 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7370 (mtm) REVERT: A 129 ARG cc_start: 0.7491 (tpt90) cc_final: 0.6998 (tpt-90) REVERT: B 79 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7833 (mmtt) REVERT: C 24 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7793 (mm-40) REVERT: C 74 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7606 (mtpt) REVERT: D 44 GLN cc_start: 0.8044 (tt0) cc_final: 0.7807 (tt0) REVERT: D 56 MET cc_start: 0.8582 (tpp) cc_final: 0.8224 (tpp) REVERT: D 79 HIS cc_start: 0.7585 (m170) cc_final: 0.7192 (t-90) REVERT: D 90 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: D 96 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.7480 (mtm110) REVERT: E 109 LEU cc_start: 0.8293 (pp) cc_final: 0.7654 (mt) REVERT: F 44 LYS cc_start: 0.8361 (tttt) cc_final: 0.8120 (tttm) REVERT: F 53 GLU cc_start: 0.7393 (tp30) cc_final: 0.7114 (tp30) REVERT: F 91 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8161 (ttmm) REVERT: F 92 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7052 (mtp-110) REVERT: G 61 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7540 (mm-30) REVERT: G 95 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7665 (tmtm) REVERT: G 99 ARG cc_start: 0.7344 (mtp180) cc_final: 0.7073 (mmm-85) REVERT: H 53 SER cc_start: 0.8721 (t) cc_final: 0.8514 (m) REVERT: H 83 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7351 (mmt90) outliers start: 14 outliers final: 6 residues processed: 131 average time/residue: 1.7631 time to fit residues: 243.9538 Evaluate side-chains 122 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 75 HIS B 93 GLN C 73 ASN E 68 GLN H 44 GLN H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 12592 Z= 0.493 Angle : 0.730 8.960 18234 Z= 0.418 Chirality : 0.046 0.175 2075 Planarity : 0.007 0.063 1319 Dihedral : 31.398 178.795 3954 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.86 % Allowed : 13.02 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 734 helix: 1.03 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.029 0.004 PHE G 25 TYR 0.018 0.003 TYR F 51 ARG 0.008 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.850 Fit side-chains REVERT: A 50 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 120 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7314 (mtm) REVERT: A 129 ARG cc_start: 0.7547 (tpt90) cc_final: 0.6862 (tpt-90) REVERT: B 92 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7704 (ttp80) REVERT: C 24 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7802 (mm-40) REVERT: C 61 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: C 74 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7462 (mtpt) REVERT: D 56 MET cc_start: 0.8585 (tpp) cc_final: 0.8199 (tpp) REVERT: D 79 HIS cc_start: 0.7568 (m170) cc_final: 0.7245 (t-90) REVERT: D 90 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: D 96 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7224 (mtm110) REVERT: D 117 LYS cc_start: 0.8229 (tttp) cc_final: 0.8019 (tttp) REVERT: E 115 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7500 (mmtp) REVERT: E 120 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: F 44 LYS cc_start: 0.8328 (tttt) cc_final: 0.8017 (tttm) REVERT: F 52 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7643 (tp30) REVERT: F 53 GLU cc_start: 0.7611 (tp30) cc_final: 0.7344 (tp30) REVERT: F 91 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8165 (ttmm) REVERT: G 36 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7583 (tmmt) REVERT: G 92 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: G 95 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7645 (tmtm) REVERT: G 99 ARG cc_start: 0.7354 (mtp180) cc_final: 0.7107 (mtp180) REVERT: H 53 SER cc_start: 0.8767 (t) cc_final: 0.8480 (m) REVERT: H 54 LYS cc_start: 0.7767 (tptt) cc_final: 0.7395 (mmmt) REVERT: H 83 ARG cc_start: 0.7867 (mmt-90) cc_final: 0.7643 (mmt90) REVERT: H 96 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7697 (mtt180) outliers start: 24 outliers final: 12 residues processed: 135 average time/residue: 1.7567 time to fit residues: 250.3170 Evaluate side-chains 142 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12592 Z= 0.190 Angle : 0.608 8.676 18234 Z= 0.366 Chirality : 0.037 0.184 2075 Planarity : 0.005 0.095 1319 Dihedral : 31.391 178.008 3954 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.54 % Allowed : 13.67 % Favored : 82.80 % 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: 1.39 (0.29), residues: 734 helix: 1.54 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 31 PHE 0.010 0.001 PHE G 25 TYR 0.013 0.002 TYR F 51 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.892 Fit side-chains REVERT: A 50 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 120 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8163 (mmt) REVERT: A 129 ARG cc_start: 0.7476 (tpt90) cc_final: 0.6668 (tpt-90) REVERT: B 92 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7681 (ttp80) REVERT: C 24 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7816 (mm-40) REVERT: C 61 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: D 56 MET cc_start: 0.8542 (tpp) cc_final: 0.8196 (tpp) REVERT: D 79 HIS cc_start: 0.7507 (m170) cc_final: 0.7227 (t-90) REVERT: D 90 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: D 96 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7200 (mtm110) REVERT: E 120 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: F 44 LYS cc_start: 0.8318 (tttt) cc_final: 0.8053 (tttm) REVERT: F 52 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7604 (tp30) REVERT: F 53 GLU cc_start: 0.7532 (tp30) cc_final: 0.7252 (tp30) REVERT: F 91 LYS cc_start: 0.8357 (ttpp) cc_final: 0.8138 (ttmm) REVERT: G 20 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7263 (ptp90) REVERT: G 36 LYS cc_start: 0.7906 (mmpt) cc_final: 0.7537 (tmmt) REVERT: G 64 GLU cc_start: 0.7362 (tt0) cc_final: 0.6912 (mm-30) REVERT: G 92 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: G 95 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7620 (tmtm) REVERT: G 99 ARG cc_start: 0.7313 (mtp180) cc_final: 0.7071 (mtp180) REVERT: H 53 SER cc_start: 0.8657 (t) cc_final: 0.8418 (m) REVERT: H 54 LYS cc_start: 0.7667 (tptt) cc_final: 0.7465 (mmtp) REVERT: H 83 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7458 (mmt90) REVERT: H 96 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7662 (mtt180) outliers start: 22 outliers final: 12 residues processed: 135 average time/residue: 1.7350 time to fit residues: 247.6635 Evaluate side-chains 139 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12592 Z= 0.229 Angle : 0.594 8.170 18234 Z= 0.356 Chirality : 0.036 0.145 2075 Planarity : 0.004 0.048 1319 Dihedral : 31.295 179.897 3954 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.38 % Allowed : 13.99 % Favored : 82.64 % 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: 1.57 (0.29), residues: 734 helix: 1.67 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.010 0.002 PHE E 67 TYR 0.013 0.002 TYR F 51 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.914 Fit side-chains REVERT: A 50 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 120 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8219 (mmt) REVERT: A 129 ARG cc_start: 0.7485 (tpt90) cc_final: 0.6778 (tpt-90) REVERT: B 92 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7689 (ttp80) REVERT: C 24 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7820 (mm-40) REVERT: C 64 GLU cc_start: 0.7660 (tp30) cc_final: 0.7307 (tm-30) REVERT: D 56 MET cc_start: 0.8571 (tpp) cc_final: 0.8200 (tpp) REVERT: D 79 HIS cc_start: 0.7536 (m170) cc_final: 0.7251 (t-90) REVERT: D 90 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: D 96 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7187 (mtm110) REVERT: E 65 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7867 (mp) REVERT: E 120 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8146 (mtt) REVERT: F 44 LYS cc_start: 0.8354 (tttt) cc_final: 0.8040 (tttm) REVERT: F 52 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7576 (tp30) REVERT: F 53 GLU cc_start: 0.7528 (tp30) cc_final: 0.7240 (tp30) REVERT: F 91 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8157 (ttmm) REVERT: G 36 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7585 (pttp) REVERT: G 64 GLU cc_start: 0.7393 (tt0) cc_final: 0.6935 (mm-30) REVERT: G 92 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: G 95 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7610 (tmtm) REVERT: G 99 ARG cc_start: 0.7320 (mtp180) cc_final: 0.7081 (mtp180) REVERT: H 53 SER cc_start: 0.8670 (t) cc_final: 0.8426 (m) REVERT: H 54 LYS cc_start: 0.7691 (tptt) cc_final: 0.7483 (mmtp) REVERT: H 83 ARG cc_start: 0.7775 (mmt-90) cc_final: 0.7488 (mmt90) REVERT: H 96 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7679 (mtt180) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 1.7764 time to fit residues: 246.0773 Evaluate side-chains 134 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12592 Z= 0.203 Angle : 0.572 7.789 18234 Z= 0.346 Chirality : 0.036 0.143 2075 Planarity : 0.004 0.047 1319 Dihedral : 31.198 179.618 3954 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.22 % Allowed : 14.95 % Favored : 81.83 % 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: 1.73 (0.29), residues: 734 helix: 1.80 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.009 0.002 PHE G 25 TYR 0.013 0.002 TYR F 51 ARG 0.004 0.001 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.841 Fit side-chains REVERT: A 50 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 120 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7349 (mtm) REVERT: A 129 ARG cc_start: 0.7456 (tpt90) cc_final: 0.6771 (tpt-90) REVERT: B 92 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7710 (ttp80) REVERT: C 24 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7725 (mm-40) REVERT: C 64 GLU cc_start: 0.7583 (tp30) cc_final: 0.7233 (tm-30) REVERT: C 75 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7725 (mmtp) REVERT: D 56 MET cc_start: 0.8569 (tpp) cc_final: 0.8196 (tpp) REVERT: D 79 HIS cc_start: 0.7541 (m170) cc_final: 0.7255 (t-90) REVERT: D 90 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: D 96 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7257 (mtm110) REVERT: E 65 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.7869 (mp) REVERT: E 109 LEU cc_start: 0.8254 (pp) cc_final: 0.7725 (mt) REVERT: E 120 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: F 44 LYS cc_start: 0.8363 (tttt) cc_final: 0.8089 (tttm) REVERT: F 52 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7558 (tp30) REVERT: F 53 GLU cc_start: 0.7513 (tp30) cc_final: 0.7176 (tp30) REVERT: F 91 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8140 (ttmm) REVERT: G 36 LYS cc_start: 0.7895 (mmpt) cc_final: 0.7574 (pttp) REVERT: G 64 GLU cc_start: 0.7414 (tt0) cc_final: 0.6940 (mm-30) REVERT: G 92 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: G 95 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7607 (tmtm) REVERT: G 99 ARG cc_start: 0.7347 (mtp180) cc_final: 0.7109 (mtp180) REVERT: H 53 SER cc_start: 0.8660 (t) cc_final: 0.8428 (m) REVERT: H 54 LYS cc_start: 0.7688 (tptt) cc_final: 0.7381 (mmtt) REVERT: H 83 ARG cc_start: 0.7793 (mmt-90) cc_final: 0.7511 (mmt90) REVERT: H 96 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7697 (mtt180) outliers start: 20 outliers final: 12 residues processed: 133 average time/residue: 1.6802 time to fit residues: 236.4774 Evaluate side-chains 137 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 38 optimal weight: 0.5980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12592 Z= 0.204 Angle : 0.561 7.438 18234 Z= 0.339 Chirality : 0.035 0.138 2075 Planarity : 0.004 0.047 1319 Dihedral : 31.095 179.922 3954 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.05 % Allowed : 15.27 % Favored : 81.67 % 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: 1.90 (0.30), residues: 734 helix: 1.89 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.56 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.009 0.002 PHE F 61 TYR 0.012 0.002 TYR F 51 ARG 0.003 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.007 Fit side-chains REVERT: A 50 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 120 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: A 129 ARG cc_start: 0.7394 (tpt90) cc_final: 0.6735 (tpt-90) REVERT: B 92 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7725 (ttp80) REVERT: C 24 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7701 (mm-40) REVERT: C 64 GLU cc_start: 0.7526 (tp30) cc_final: 0.7201 (tm-30) REVERT: C 75 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7744 (mmtp) REVERT: D 56 MET cc_start: 0.8568 (tpp) cc_final: 0.8179 (tpp) REVERT: D 79 HIS cc_start: 0.7540 (m170) cc_final: 0.7253 (t-90) REVERT: D 90 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: D 96 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7264 (mtm110) REVERT: E 65 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.7882 (mp) REVERT: E 109 LEU cc_start: 0.8220 (pp) cc_final: 0.7757 (mt) REVERT: E 120 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: F 44 LYS cc_start: 0.8356 (tttt) cc_final: 0.8040 (tttm) REVERT: F 52 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7562 (tp30) REVERT: F 53 GLU cc_start: 0.7509 (tp30) cc_final: 0.7179 (tp30) REVERT: F 79 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8099 (mtpt) REVERT: F 91 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8135 (ttmm) REVERT: G 36 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7607 (pttp) REVERT: G 64 GLU cc_start: 0.7412 (tt0) cc_final: 0.6950 (mm-30) REVERT: G 92 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: G 95 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7608 (tmtm) REVERT: G 99 ARG cc_start: 0.7370 (mtp180) cc_final: 0.7149 (mtp180) REVERT: H 53 SER cc_start: 0.8658 (t) cc_final: 0.8429 (m) REVERT: H 83 ARG cc_start: 0.7806 (mmt-90) cc_final: 0.7544 (mmt90) REVERT: H 96 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7702 (mtt180) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 1.7684 time to fit residues: 248.5245 Evaluate side-chains 137 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12592 Z= 0.224 Angle : 0.563 7.382 18234 Z= 0.339 Chirality : 0.035 0.136 2075 Planarity : 0.004 0.047 1319 Dihedral : 30.989 179.617 3954 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.22 % Allowed : 15.76 % Favored : 81.03 % 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: 1.98 (0.30), residues: 734 helix: 1.95 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.54 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 39 PHE 0.009 0.002 PHE F 100 TYR 0.014 0.002 TYR F 51 ARG 0.003 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.834 Fit side-chains REVERT: A 50 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 120 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: A 129 ARG cc_start: 0.7456 (tpt90) cc_final: 0.6798 (tpt-90) REVERT: B 92 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7731 (ttp80) REVERT: C 64 GLU cc_start: 0.7496 (tp30) cc_final: 0.7230 (tm-30) REVERT: C 75 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7787 (mmtp) REVERT: C 114 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7610 (p) REVERT: D 56 MET cc_start: 0.8575 (tpp) cc_final: 0.8165 (tpp) REVERT: D 79 HIS cc_start: 0.7537 (m170) cc_final: 0.7250 (t-90) REVERT: D 82 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7746 (mmtp) REVERT: D 90 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: D 96 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7266 (mtm110) REVERT: E 65 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.7911 (mp) REVERT: E 109 LEU cc_start: 0.8214 (pp) cc_final: 0.7768 (mt) REVERT: E 120 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: F 44 LYS cc_start: 0.8388 (tttt) cc_final: 0.8071 (tttm) REVERT: F 52 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7571 (tp30) REVERT: F 53 GLU cc_start: 0.7519 (tp30) cc_final: 0.7177 (tp30) REVERT: F 79 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8097 (mtpt) REVERT: F 91 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8142 (ttmm) REVERT: G 19 SER cc_start: 0.8759 (p) cc_final: 0.8408 (p) REVERT: G 36 LYS cc_start: 0.7928 (mmpt) cc_final: 0.7700 (pttp) REVERT: G 64 GLU cc_start: 0.7403 (tt0) cc_final: 0.6784 (mm-30) REVERT: G 95 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7605 (tmtm) REVERT: G 99 ARG cc_start: 0.7343 (mtp180) cc_final: 0.7083 (mmm-85) REVERT: H 53 SER cc_start: 0.8674 (t) cc_final: 0.8439 (m) REVERT: H 54 LYS cc_start: 0.7690 (tptt) cc_final: 0.7380 (mmtt) REVERT: H 83 ARG cc_start: 0.7795 (mmt-90) cc_final: 0.7534 (mmt90) REVERT: H 96 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7631 (mtt180) outliers start: 20 outliers final: 14 residues processed: 135 average time/residue: 1.8494 time to fit residues: 263.2591 Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12592 Z= 0.335 Angle : 0.622 8.296 18234 Z= 0.367 Chirality : 0.039 0.142 2075 Planarity : 0.005 0.049 1319 Dihedral : 31.139 179.167 3954 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.22 % Allowed : 16.24 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 734 helix: 1.68 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 39 PHE 0.012 0.002 PHE G 25 TYR 0.016 0.002 TYR F 51 ARG 0.004 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.738 Fit side-chains REVERT: A 50 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 120 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7362 (mtm) REVERT: A 129 ARG cc_start: 0.7418 (tpt90) cc_final: 0.6741 (tpt-90) REVERT: B 92 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7764 (ttp80) REVERT: C 64 GLU cc_start: 0.7572 (tp30) cc_final: 0.7293 (tm-30) REVERT: C 75 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7818 (mmtp) REVERT: C 114 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7595 (p) REVERT: D 56 MET cc_start: 0.8578 (tpp) cc_final: 0.8191 (tpp) REVERT: D 65 ASP cc_start: 0.8898 (t70) cc_final: 0.8368 (t0) REVERT: D 79 HIS cc_start: 0.7602 (m170) cc_final: 0.7304 (t-90) REVERT: D 90 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: D 96 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7268 (mtm110) REVERT: E 65 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.7926 (mp) REVERT: E 120 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8285 (mtt) REVERT: F 44 LYS cc_start: 0.8379 (tttt) cc_final: 0.8046 (tttm) REVERT: F 52 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7632 (tp30) REVERT: F 53 GLU cc_start: 0.7613 (tp30) cc_final: 0.7272 (tp30) REVERT: F 91 LYS cc_start: 0.8344 (ttpp) cc_final: 0.8114 (ttmm) REVERT: G 36 LYS cc_start: 0.7968 (mmpt) cc_final: 0.7733 (pttp) REVERT: G 64 GLU cc_start: 0.7435 (tt0) cc_final: 0.6968 (mm-30) REVERT: G 95 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7629 (tmtm) REVERT: G 99 ARG cc_start: 0.7334 (mtp180) cc_final: 0.7119 (mtp180) REVERT: H 53 SER cc_start: 0.8730 (t) cc_final: 0.8461 (m) REVERT: H 83 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7551 (mmt90) REVERT: H 96 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7713 (mtt180) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 1.7711 time to fit residues: 248.7760 Evaluate side-chains 139 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0670 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12592 Z= 0.175 Angle : 0.579 8.021 18234 Z= 0.349 Chirality : 0.035 0.145 2075 Planarity : 0.004 0.045 1319 Dihedral : 31.152 179.679 3954 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.73 % Allowed : 16.72 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.30), residues: 734 helix: 1.87 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.62 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.010 0.002 PHE F 61 TYR 0.014 0.002 TYR F 51 ARG 0.004 0.001 ARG G 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.950 Fit side-chains REVERT: A 50 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 120 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7350 (mtm) REVERT: A 129 ARG cc_start: 0.7400 (tpt90) cc_final: 0.6718 (tpt-90) REVERT: B 92 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7772 (ttp80) REVERT: C 64 GLU cc_start: 0.7501 (tp30) cc_final: 0.7235 (tm-30) REVERT: C 76 THR cc_start: 0.8102 (p) cc_final: 0.7731 (p) REVERT: C 114 VAL cc_start: 0.7967 (m) cc_final: 0.7615 (p) REVERT: D 56 MET cc_start: 0.8558 (tpp) cc_final: 0.8170 (tpp) REVERT: D 65 ASP cc_start: 0.8859 (t70) cc_final: 0.8308 (t0) REVERT: D 79 HIS cc_start: 0.7552 (m170) cc_final: 0.7286 (t-90) REVERT: D 90 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: D 96 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7275 (mtm110) REVERT: E 65 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7885 (mp) REVERT: E 120 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8093 (mtt) REVERT: F 44 LYS cc_start: 0.8369 (tttt) cc_final: 0.8063 (tttm) REVERT: F 52 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7588 (tp30) REVERT: F 53 GLU cc_start: 0.7540 (tp30) cc_final: 0.7186 (tp30) REVERT: F 91 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8117 (ttmm) REVERT: G 36 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7721 (pttp) REVERT: G 64 GLU cc_start: 0.7404 (tt0) cc_final: 0.6951 (mm-30) REVERT: G 95 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7613 (tmtm) REVERT: G 99 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7058 (mmm-85) REVERT: H 53 SER cc_start: 0.8697 (t) cc_final: 0.8445 (m) REVERT: H 83 ARG cc_start: 0.7750 (mmt-90) cc_final: 0.7455 (mmt90) REVERT: H 96 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7641 (mtt180) outliers start: 17 outliers final: 12 residues processed: 135 average time/residue: 1.7746 time to fit residues: 252.8773 Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127944 restraints weight = 10870.191| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 0.65 r_work: 0.2976 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12592 Z= 0.210 Angle : 0.575 8.076 18234 Z= 0.346 Chirality : 0.036 0.140 2075 Planarity : 0.004 0.046 1319 Dihedral : 31.140 179.453 3954 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.22 % Allowed : 16.08 % Favored : 80.71 % 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: 1.89 (0.30), residues: 734 helix: 1.89 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.58 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.010 0.002 PHE F 61 TYR 0.014 0.002 TYR F 51 ARG 0.003 0.000 ARG B 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4211.36 seconds wall clock time: 74 minutes 34.89 seconds (4474.89 seconds total)