Starting phenix.real_space_refine on Wed Sep 25 23:25:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/09_2024/7ohc_12900.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 289 5.49 5 S 12 5.16 5 C 6648 2.51 5 N 2262 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.80, per 1000 atoms: 0.57 Number of scatterers: 12019 At special positions: 0 Unit cell: (74.55, 119.7, 115.5, 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 289 15.00 O 2808 8.00 N 2262 7.00 C 6648 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 874.5 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.3% alpha, 3.1% beta 144 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.244A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 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 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.340A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.030A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.355A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.461A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.407A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 3.22 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: 1813 1.33 - 1.45: 4503 1.45 - 1.57: 5904 1.57 - 1.69: 580 1.69 - 1.81: 22 Bond restraints: 12822 Sorted by residual: bond pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.41e+01 bond pdb=" CG GLU H 110 " pdb=" CD GLU H 110 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.24e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.57e+00 bond pdb=" CD GLU H 110 " pdb=" OE2 GLU H 110 " ideal model delta sigma weight residual 1.249 1.209 0.040 1.90e-02 2.77e+03 4.39e+00 ... (remaining 12817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17923 2.09 - 4.17: 563 4.17 - 6.26: 40 6.26 - 8.34: 19 8.34 - 10.43: 11 Bond angle restraints: 18556 Sorted by residual: angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.03e+01 angle pdb=" C ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 119.26 -8.70 1.69e+00 3.50e-01 2.65e+01 angle pdb=" CA THR A 58 " pdb=" CB THR A 58 " pdb=" CG2 THR A 58 " ideal model delta sigma weight residual 110.50 118.23 -7.73 1.70e+00 3.46e-01 2.07e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 104.19 6.37 1.46e+00 4.69e-01 1.90e+01 angle pdb=" CA LYS G 74 " pdb=" CB LYS G 74 " pdb=" CG LYS G 74 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 ... (remaining 18551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4465 21.47 - 42.93: 1384 42.93 - 64.40: 1085 64.40 - 85.87: 47 85.87 - 107.34: 4 Dihedral angle restraints: 6985 sinusoidal: 4767 harmonic: 2218 Sorted by residual: 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 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+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 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1910 0.082 - 0.165: 191 0.165 - 0.247: 9 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CB THR D 116 " pdb=" CA THR D 116 " pdb=" OG1 THR D 116 " pdb=" CG2 THR D 116 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2108 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN C 73 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR A 58 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.036 2.00e-02 2.50e+03 2.11e-02 9.97e+00 pdb=" N1 DC I 69 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.010 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 951 2.73 - 3.28: 10386 3.28 - 3.82: 24870 3.82 - 4.36: 30273 4.36 - 4.90: 41885 Nonbonded interactions: 108365 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.238 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.255 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.275 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.299 3.040 ... (remaining 108360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) 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=0.00 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: 0.470 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.000 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.005 0.113 12822 Z= 0.314 Angle : 0.856 10.429 18556 Z= 0.503 Chirality : 0.049 0.412 2111 Planarity : 0.006 0.052 1344 Dihedral : 29.622 107.336 5553 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.16 % Allowed : 15.70 % Favored : 84.14 % 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: 0.04 (0.27), residues: 748 helix: 0.44 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.029 0.003 PHE G 25 TYR 0.051 0.003 TYR H 118 ARG 0.014 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 0.897 Fit side-chains REVERT: A 42 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7580 (mmm-85) REVERT: A 50 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 90 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t0) REVERT: D 31 LYS cc_start: 0.8728 (mptt) cc_final: 0.8420 (mmtm) REVERT: D 68 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tp30) REVERT: D 90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7932 (mp0) REVERT: D 105 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8266 (ttpp) REVERT: E 129 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8010 (tpt90) REVERT: G 74 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8400 (mtmm) REVERT: G 99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7691 (mmm-85) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8469 (t0) REVERT: H 76 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7532 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 1.7261 time to fit residues: 374.1800 Evaluate side-chains 184 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12822 Z= 0.338 Angle : 0.622 5.737 18556 Z= 0.373 Chirality : 0.038 0.170 2111 Planarity : 0.005 0.046 1344 Dihedral : 31.626 106.575 4030 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.83 % Allowed : 17.27 % Favored : 79.91 % 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: 1.58 (0.29), residues: 748 helix: 1.61 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.023 0.002 PHE G 25 TYR 0.017 0.002 TYR H 37 ARG 0.006 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 0.980 Fit side-chains REVERT: A 42 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7255 (mmm-85) REVERT: A 50 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 123 ASP cc_start: 0.8778 (m-30) cc_final: 0.8577 (m-30) REVERT: B 68 ASP cc_start: 0.8316 (m-30) cc_final: 0.8103 (m-30) REVERT: B 79 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8503 (mttm) REVERT: C 64 GLU cc_start: 0.7918 (tt0) cc_final: 0.7629 (tp30) REVERT: C 73 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8469 (t0) REVERT: C 90 ASP cc_start: 0.8183 (t70) cc_final: 0.7854 (t70) REVERT: D 68 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7453 (tp30) REVERT: D 90 GLU cc_start: 0.8368 (mp0) cc_final: 0.8026 (mp0) REVERT: E 68 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: E 129 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7824 (tpt90) REVERT: F 63 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: G 113 SER cc_start: 0.9029 (m) cc_final: 0.8807 (p) REVERT: H 39 TYR cc_start: 0.7698 (t80) cc_final: 0.7410 (t80) REVERT: H 65 ASP cc_start: 0.8738 (t70) cc_final: 0.8446 (t0) REVERT: H 76 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7647 (mtm-85) outliers start: 18 outliers final: 4 residues processed: 192 average time/residue: 1.7092 time to fit residues: 347.3048 Evaluate side-chains 186 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12822 Z= 0.328 Angle : 0.605 5.620 18556 Z= 0.365 Chirality : 0.037 0.178 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.351 114.637 4030 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.77 % Allowed : 18.52 % Favored : 77.71 % 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: 2.08 (0.29), residues: 748 helix: 1.99 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE G 25 TYR 0.013 0.002 TYR D 37 ARG 0.006 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8761 (m-30) cc_final: 0.8535 (m-30) REVERT: B 79 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8481 (mttm) REVERT: C 64 GLU cc_start: 0.7936 (tt0) cc_final: 0.7605 (tp30) REVERT: C 73 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 90 ASP cc_start: 0.8128 (t70) cc_final: 0.7819 (t70) REVERT: C 91 GLU cc_start: 0.7809 (pm20) cc_final: 0.7599 (pm20) REVERT: E 68 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: E 115 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8745 (mtpt) REVERT: E 120 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7281 (mpp) REVERT: H 30 ARG cc_start: 0.6722 (mtp-110) cc_final: 0.6476 (mtt180) REVERT: H 39 TYR cc_start: 0.7743 (t80) cc_final: 0.7359 (t80) REVERT: H 65 ASP cc_start: 0.8692 (t70) cc_final: 0.8420 (t0) REVERT: H 76 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: H 110 GLU cc_start: 0.7755 (pt0) cc_final: 0.7547 (pt0) outliers start: 24 outliers final: 12 residues processed: 189 average time/residue: 1.7519 time to fit residues: 350.0286 Evaluate side-chains 193 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12822 Z= 0.312 Angle : 0.594 8.277 18556 Z= 0.358 Chirality : 0.036 0.142 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.140 124.525 4030 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.61 % Allowed : 21.19 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.30), residues: 748 helix: 2.13 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE G 25 TYR 0.011 0.002 TYR D 37 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 0.885 Fit side-chains REVERT: A 123 ASP cc_start: 0.8755 (m-30) cc_final: 0.8494 (m-30) REVERT: B 79 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: C 73 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 90 ASP cc_start: 0.8171 (t70) cc_final: 0.7831 (t70) REVERT: D 54 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8460 (mmtp) REVERT: E 68 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: E 120 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7251 (mpp) REVERT: F 92 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7830 (ttp80) REVERT: G 74 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8425 (mtmm) REVERT: G 92 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7881 (mt-10) REVERT: H 30 ARG cc_start: 0.6889 (mtp-110) cc_final: 0.6647 (mtt180) REVERT: H 39 TYR cc_start: 0.7734 (t80) cc_final: 0.7406 (t80) REVERT: H 65 ASP cc_start: 0.8689 (t70) cc_final: 0.8444 (t0) REVERT: H 76 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7514 (mtm-85) outliers start: 23 outliers final: 11 residues processed: 191 average time/residue: 1.7528 time to fit residues: 353.5622 Evaluate side-chains 195 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12822 Z= 0.207 Angle : 0.585 6.440 18556 Z= 0.354 Chirality : 0.034 0.146 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.164 125.222 4030 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.30 % Allowed : 21.19 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.30), residues: 748 helix: 2.29 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.023 0.002 TYR G 57 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.130 Fit side-chains REVERT: A 42 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7758 (mtp85) REVERT: A 123 ASP cc_start: 0.8718 (m-30) cc_final: 0.8474 (m-30) REVERT: B 79 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8487 (mttm) REVERT: C 64 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7652 (tp30) REVERT: C 73 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8250 (t0) REVERT: C 90 ASP cc_start: 0.8161 (t70) cc_final: 0.7818 (t70) REVERT: D 54 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8380 (mmtp) REVERT: E 68 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: E 120 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7214 (mpp) REVERT: F 93 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: G 74 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8422 (mtmm) REVERT: H 30 ARG cc_start: 0.6855 (mtp-110) cc_final: 0.6642 (mtt180) REVERT: H 39 TYR cc_start: 0.7657 (t80) cc_final: 0.7324 (t80) REVERT: H 65 ASP cc_start: 0.8672 (t70) cc_final: 0.8424 (t0) REVERT: H 76 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7611 (mtm-85) REVERT: H 83 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8178 (mmt180) outliers start: 21 outliers final: 11 residues processed: 186 average time/residue: 1.7583 time to fit residues: 345.2825 Evaluate side-chains 196 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12822 Z= 0.220 Angle : 0.571 6.423 18556 Z= 0.348 Chirality : 0.034 0.139 2111 Planarity : 0.004 0.052 1344 Dihedral : 31.029 126.338 4030 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.14 % Allowed : 21.98 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 748 helix: 2.35 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.017 0.002 TYR F 88 ARG 0.008 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.914 Fit side-chains REVERT: A 42 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7762 (mtp85) REVERT: A 123 ASP cc_start: 0.8767 (m-30) cc_final: 0.8529 (m-30) REVERT: B 79 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8472 (mttm) REVERT: C 73 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8264 (t0) REVERT: C 90 ASP cc_start: 0.8140 (t70) cc_final: 0.7782 (t70) REVERT: D 31 LYS cc_start: 0.8851 (mppt) cc_final: 0.8386 (mppt) REVERT: E 120 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: F 93 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: G 74 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8426 (mtmm) REVERT: G 92 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7934 (mt-10) REVERT: H 39 TYR cc_start: 0.7674 (t80) cc_final: 0.7383 (t80) REVERT: H 65 ASP cc_start: 0.8637 (t70) cc_final: 0.8377 (t0) REVERT: H 76 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7566 (mtm-85) REVERT: H 83 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8241 (mmt180) outliers start: 20 outliers final: 10 residues processed: 185 average time/residue: 1.7511 time to fit residues: 342.5655 Evaluate side-chains 194 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN D 44 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12822 Z= 0.212 Angle : 0.569 6.380 18556 Z= 0.347 Chirality : 0.034 0.139 2111 Planarity : 0.004 0.047 1344 Dihedral : 30.976 126.839 4030 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 22.61 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.30), residues: 748 helix: 2.40 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.017 0.002 TYR G 57 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 0.981 Fit side-chains REVERT: A 42 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7771 (mtp85) REVERT: A 123 ASP cc_start: 0.8752 (m-30) cc_final: 0.8524 (m-30) REVERT: B 79 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8467 (mttm) REVERT: C 73 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8292 (t0) REVERT: C 90 ASP cc_start: 0.8128 (t70) cc_final: 0.7773 (t70) REVERT: F 92 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: F 93 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: G 74 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8434 (mtmm) REVERT: G 92 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7894 (mt-10) REVERT: H 39 TYR cc_start: 0.7720 (t80) cc_final: 0.7379 (t80) REVERT: H 65 ASP cc_start: 0.8634 (t70) cc_final: 0.8380 (t0) REVERT: H 76 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7518 (mtm-85) REVERT: H 83 ARG cc_start: 0.8625 (mmt90) cc_final: 0.8246 (mmt180) outliers start: 17 outliers final: 8 residues processed: 185 average time/residue: 1.8482 time to fit residues: 360.9240 Evaluate side-chains 193 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12822 Z= 0.281 Angle : 0.583 6.065 18556 Z= 0.352 Chirality : 0.035 0.141 2111 Planarity : 0.004 0.050 1344 Dihedral : 30.931 126.972 4030 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.67 % Allowed : 22.61 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 748 helix: 2.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE G 25 TYR 0.022 0.002 TYR G 57 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.001 Fit side-chains REVERT: A 42 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7774 (mtp85) REVERT: A 123 ASP cc_start: 0.8757 (m-30) cc_final: 0.8501 (m-30) REVERT: B 79 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8474 (mttm) REVERT: C 73 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8313 (t0) REVERT: C 90 ASP cc_start: 0.8128 (t70) cc_final: 0.7759 (t70) REVERT: F 92 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7748 (ttp80) REVERT: F 93 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: G 64 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: G 74 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8435 (mtmm) REVERT: H 39 TYR cc_start: 0.7735 (t80) cc_final: 0.7393 (t80) REVERT: H 65 ASP cc_start: 0.8667 (t70) cc_final: 0.8404 (t0) REVERT: H 76 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: H 83 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8262 (mmt180) outliers start: 17 outliers final: 9 residues processed: 184 average time/residue: 1.7910 time to fit residues: 348.0601 Evaluate side-chains 194 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12822 Z= 0.271 Angle : 0.587 6.794 18556 Z= 0.355 Chirality : 0.035 0.141 2111 Planarity : 0.004 0.053 1344 Dihedral : 30.944 131.812 4030 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.51 % Allowed : 22.92 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 748 helix: 2.39 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.21 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE E 67 TYR 0.023 0.002 TYR F 88 ARG 0.009 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 0.902 Fit side-chains REVERT: A 42 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7828 (mtp85) REVERT: A 123 ASP cc_start: 0.8774 (m-30) cc_final: 0.8506 (m-30) REVERT: B 79 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8476 (mttm) REVERT: C 64 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7672 (tp30) REVERT: C 73 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8366 (t0) REVERT: C 90 ASP cc_start: 0.8137 (t70) cc_final: 0.7817 (t70) REVERT: F 92 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: F 93 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: G 74 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8432 (mtmm) REVERT: G 92 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7771 (mt-10) REVERT: H 39 TYR cc_start: 0.7713 (t80) cc_final: 0.7384 (t80) REVERT: H 65 ASP cc_start: 0.8686 (t70) cc_final: 0.8438 (t0) REVERT: H 76 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7541 (mtm-85) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 1.8049 time to fit residues: 350.5302 Evaluate side-chains 190 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12822 Z= 0.218 Angle : 0.595 8.247 18556 Z= 0.357 Chirality : 0.034 0.141 2111 Planarity : 0.004 0.050 1344 Dihedral : 30.962 132.048 4030 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.20 % Allowed : 23.86 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 748 helix: 2.43 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.24 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.034 0.002 TYR F 88 ARG 0.009 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.062 Fit side-chains REVERT: A 42 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7833 (mtp85) REVERT: A 123 ASP cc_start: 0.8757 (m-30) cc_final: 0.8500 (m-30) REVERT: B 79 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8467 (mttm) REVERT: C 64 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7654 (tp30) REVERT: C 73 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8359 (t0) REVERT: C 90 ASP cc_start: 0.8124 (t70) cc_final: 0.7780 (t70) REVERT: F 92 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7778 (ttp80) REVERT: F 93 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: G 74 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: G 92 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7747 (mt-10) REVERT: H 39 TYR cc_start: 0.7683 (t80) cc_final: 0.7355 (t80) REVERT: H 65 ASP cc_start: 0.8675 (t70) cc_final: 0.8432 (t0) REVERT: H 76 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7508 (mtm-85) REVERT: H 113 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8525 (pttm) outliers start: 14 outliers final: 8 residues processed: 181 average time/residue: 1.8135 time to fit residues: 346.6668 Evaluate side-chains 190 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 44 GLN ** E 68 GLN ** 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 = 0.3664 r_free = 0.3664 target = 0.103605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082518 restraints weight = 20441.044| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.33 r_work: 0.3126 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12822 Z= 0.252 Angle : 0.591 6.927 18556 Z= 0.356 Chirality : 0.035 0.140 2111 Planarity : 0.004 0.051 1344 Dihedral : 30.896 133.231 4030 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.35 % Allowed : 23.70 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.30), residues: 748 helix: 2.36 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.26 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.022 0.002 TYR F 88 ARG 0.010 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5358.26 seconds wall clock time: 93 minutes 53.29 seconds (5633.29 seconds total)