Starting phenix.real_space_refine on Sat Jul 20 15:44:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jld_36393/07_2024/8jld_36393.cif" } resolution = 2.48 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= 0.006 sd= 0.049 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 10 5.16 5 C 6540 2.51 5 N 2221 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 92": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 6.76, per 1000 atoms: 0.57 Number of scatterers: 11844 At special positions: 0 Unit cell: (118.72, 110.24, 116.6, 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 10 16.00 P 289 15.00 O 2784 8.00 N 2221 7.00 C 6540 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: 6.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.005A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 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 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.452A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.063A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.475A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.051A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.181A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 removed outlier: 6.492A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.042A 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: 7.240A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2608 1.34 - 1.46: 4027 1.46 - 1.58: 5413 1.58 - 1.70: 577 1.70 - 1.82: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" N LYS H 46 " pdb=" CA LYS H 46 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.33e-02 5.65e+03 4.67e+00 bond pdb=" N ARG A 129 " pdb=" CA ARG A 129 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 3.90e+00 bond pdb=" N GLU G 64 " pdb=" CA GLU G 64 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.82e+00 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 98.01 - 104.93: 1208 104.93 - 111.85: 6713 111.85 - 118.77: 3414 118.77 - 125.69: 6021 125.69 - 132.60: 965 Bond angle restraints: 18321 Sorted by residual: angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.34 118.20 -6.86 1.82e+00 3.02e-01 1.42e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.34 117.68 -6.34 1.82e+00 3.02e-01 1.21e+01 angle pdb=" CG ARG G 35 " pdb=" CD ARG G 35 " pdb=" NE ARG G 35 " ideal model delta sigma weight residual 112.00 119.39 -7.39 2.20e+00 2.07e-01 1.13e+01 angle pdb=" CA MET D 59 " pdb=" CB MET D 59 " pdb=" CG MET D 59 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.82e+00 angle pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" O ARG A 129 " ideal model delta sigma weight residual 120.90 117.85 3.05 1.07e+00 8.73e-01 8.15e+00 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 4330 21.29 - 42.58: 1362 42.58 - 63.88: 1107 63.88 - 85.17: 46 85.17 - 106.46: 4 Dihedral angle restraints: 6849 sinusoidal: 4697 harmonic: 2152 Sorted by residual: dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 60.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual 90.00 42.05 47.95 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.79 44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1329 0.033 - 0.067: 499 0.067 - 0.100: 190 0.100 - 0.133: 54 0.133 - 0.166: 11 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA GLU G 64 " pdb=" N GLU G 64 " pdb=" C GLU G 64 " pdb=" CB GLU G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 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 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG A 129 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 95 " 0.422 9.50e-02 1.11e+02 1.89e-01 2.19e+01 pdb=" NE ARG B 95 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 95 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 95 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 95 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " 0.016 2.00e-02 2.50e+03 1.71e-02 6.58e+00 pdb=" N1 DC J 19 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.004 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 7925 3.12 - 3.72: 20865 3.72 - 4.31: 30867 4.31 - 4.90: 43915 Nonbonded interactions: 103591 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 1.941 2.440 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.114 2.496 nonbonded pdb=" NH1 ARG C 11 " pdb=" O2 DT I -42 " model vdw 2.217 2.520 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR G 39 " pdb=" OE2 GLU H 71 " model vdw 2.297 2.440 ... (remaining 103586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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: 0.380 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.820 Find NCS groups from input model: 0.250 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.004 0.040 12645 Z= 0.213 Angle : 0.706 7.717 18321 Z= 0.442 Chirality : 0.042 0.166 2083 Planarity : 0.014 0.424 1316 Dihedral : 29.740 106.461 5465 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 17.37 % Favored : 82.31 % 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: 0.65 (0.27), residues: 730 helix: 0.79 (0.20), residues: 538 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.002 TYR F 51 ARG 0.012 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.847 Fit side-chains REVERT: G 73 ASN cc_start: 0.8425 (t0) cc_final: 0.8170 (t0) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 1.9941 time to fit residues: 340.9384 Evaluate side-chains 151 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12645 Z= 0.310 Angle : 0.609 5.463 18321 Z= 0.373 Chirality : 0.038 0.128 2083 Planarity : 0.004 0.033 1316 Dihedral : 30.810 100.632 4005 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.60 % Allowed : 18.02 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.31), residues: 730 helix: 2.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.009 0.002 TYR G 57 ARG 0.007 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8391 (ttm170) REVERT: A 83 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8223 (mtt90) REVERT: C 73 ASN cc_start: 0.8441 (t0) cc_final: 0.8106 (t160) REVERT: E 40 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8215 (mtp85) REVERT: E 83 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7770 (mtm180) REVERT: F 84 MET cc_start: 0.8742 (mmm) cc_final: 0.8540 (mmp) REVERT: F 92 ARG cc_start: 0.9067 (ptm-80) cc_final: 0.8862 (ptm-80) REVERT: G 73 ASN cc_start: 0.8476 (t0) cc_final: 0.8207 (t0) REVERT: G 91 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.3778 (tp30) outliers start: 16 outliers final: 7 residues processed: 169 average time/residue: 1.9640 time to fit residues: 348.6927 Evaluate side-chains 169 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 47 GLN D 63 ASN D 95 GLN E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12645 Z= 0.300 Angle : 0.589 6.570 18321 Z= 0.363 Chirality : 0.037 0.130 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.480 96.308 4003 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.73 % Allowed : 16.72 % Favored : 79.55 % 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: 3.17 (0.30), residues: 730 helix: 2.90 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.011 0.002 PHE A 67 TYR 0.009 0.002 TYR G 57 ARG 0.005 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8346 (ttm170) REVERT: B 35 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8280 (mtp85) REVERT: B 93 GLN cc_start: 0.8296 (mt0) cc_final: 0.7944 (mp10) REVERT: C 73 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8141 (t160) REVERT: C 91 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5806 (mp0) REVERT: E 83 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7821 (mtm180) REVERT: F 84 MET cc_start: 0.8792 (mmm) cc_final: 0.8545 (mmp) REVERT: G 73 ASN cc_start: 0.8482 (t0) cc_final: 0.8187 (t0) REVERT: G 91 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.3664 (tp30) outliers start: 23 outliers final: 10 residues processed: 171 average time/residue: 1.9273 time to fit residues: 346.1188 Evaluate side-chains 173 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 12645 Z= 0.312 Angle : 0.590 5.521 18321 Z= 0.363 Chirality : 0.037 0.137 2083 Planarity : 0.004 0.033 1316 Dihedral : 30.352 96.029 4003 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.22 % Allowed : 18.02 % Favored : 77.76 % 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: 3.11 (0.30), residues: 730 helix: 2.85 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.002 TYR F 88 ARG 0.004 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8401 (ttm170) REVERT: B 35 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8258 (mtp85) REVERT: B 93 GLN cc_start: 0.8348 (mt0) cc_final: 0.7965 (mp10) REVERT: B 95 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7980 (mtp-110) REVERT: C 11 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7171 (pmm-80) REVERT: C 73 ASN cc_start: 0.8526 (t0) cc_final: 0.8182 (t160) REVERT: C 91 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: C 99 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7442 (mtm110) REVERT: E 83 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7881 (mtm180) REVERT: G 73 ASN cc_start: 0.8497 (t0) cc_final: 0.8226 (t0) REVERT: G 91 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.3751 (tp30) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 1.9351 time to fit residues: 350.2083 Evaluate side-chains 181 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12645 Z= 0.257 Angle : 0.581 5.704 18321 Z= 0.358 Chirality : 0.036 0.130 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.362 96.056 4003 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 19.48 % Favored : 77.11 % 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: 3.17 (0.30), residues: 730 helix: 2.89 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.008 0.001 TYR B 51 ARG 0.005 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.824 Fit side-chains REVERT: A 40 ARG cc_start: 0.8670 (mtp-110) cc_final: 0.8421 (ttm170) REVERT: A 83 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8210 (mtt90) REVERT: B 35 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8282 (mtp85) REVERT: B 95 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7969 (mtp-110) REVERT: C 11 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7215 (pmm-80) REVERT: C 73 ASN cc_start: 0.8513 (t0) cc_final: 0.8165 (t160) REVERT: C 91 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: G 73 ASN cc_start: 0.8484 (t0) cc_final: 0.8207 (t0) REVERT: G 91 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.3723 (tp30) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 2.0240 time to fit residues: 356.9766 Evaluate side-chains 173 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12645 Z= 0.270 Angle : 0.580 10.240 18321 Z= 0.357 Chirality : 0.036 0.134 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.342 95.982 4003 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 19.64 % Favored : 76.95 % 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: 3.17 (0.30), residues: 730 helix: 2.88 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR H 121 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 0.774 Fit side-chains REVERT: A 40 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8463 (ttm170) REVERT: B 35 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8284 (mtp85) REVERT: B 93 GLN cc_start: 0.8247 (mt0) cc_final: 0.7847 (mp10) REVERT: B 95 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7982 (mtp-110) REVERT: C 11 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7289 (pmm-80) REVERT: C 73 ASN cc_start: 0.8514 (t0) cc_final: 0.8163 (t160) REVERT: C 91 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: E 83 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7818 (mtm180) REVERT: G 73 ASN cc_start: 0.8484 (t0) cc_final: 0.8204 (t0) REVERT: G 91 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.3722 (tp30) outliers start: 21 outliers final: 14 residues processed: 166 average time/residue: 1.9484 time to fit residues: 339.7215 Evaluate side-chains 175 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12645 Z= 0.188 Angle : 0.564 5.202 18321 Z= 0.351 Chirality : 0.034 0.124 2083 Planarity : 0.004 0.029 1316 Dihedral : 30.369 95.883 4003 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.06 % Allowed : 19.48 % Favored : 76.46 % 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: 3.32 (0.31), residues: 730 helix: 3.00 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.009 0.001 TYR D 40 ARG 0.002 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.871 Fit side-chains REVERT: A 40 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8471 (ttm170) REVERT: A 83 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8206 (mtt90) REVERT: A 129 ARG cc_start: 0.8135 (mmm160) cc_final: 0.7777 (tpt90) REVERT: B 95 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7967 (mtp-110) REVERT: C 11 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7260 (pmm-80) REVERT: C 73 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8142 (t160) REVERT: C 91 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5770 (mp0) REVERT: F 93 GLN cc_start: 0.8488 (mt0) cc_final: 0.8255 (mt0) REVERT: G 73 ASN cc_start: 0.8471 (t0) cc_final: 0.8188 (t0) REVERT: G 91 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.3622 (tp30) outliers start: 25 outliers final: 14 residues processed: 171 average time/residue: 1.9596 time to fit residues: 351.8781 Evaluate side-chains 176 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12645 Z= 0.311 Angle : 0.591 9.547 18321 Z= 0.362 Chirality : 0.037 0.143 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.269 96.161 4003 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.73 % Allowed : 19.97 % Favored : 76.30 % 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: 3.12 (0.30), residues: 730 helix: 2.85 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.013 0.002 TYR H 121 ARG 0.004 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.891 Fit side-chains REVERT: A 40 ARG cc_start: 0.8700 (mtp-110) cc_final: 0.8471 (ttm170) REVERT: A 83 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8210 (mtt90) REVERT: B 93 GLN cc_start: 0.8338 (mt0) cc_final: 0.7951 (mp10) REVERT: B 95 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8029 (mtp-110) REVERT: C 11 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7285 (pmm-80) REVERT: C 73 ASN cc_start: 0.8531 (t0) cc_final: 0.8175 (t160) REVERT: C 91 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: G 73 ASN cc_start: 0.8499 (t0) cc_final: 0.8221 (t0) REVERT: G 91 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.3694 (tp30) outliers start: 23 outliers final: 13 residues processed: 170 average time/residue: 1.9703 time to fit residues: 351.5769 Evaluate side-chains 175 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12645 Z= 0.305 Angle : 0.589 6.561 18321 Z= 0.361 Chirality : 0.037 0.143 2083 Planarity : 0.004 0.032 1316 Dihedral : 30.274 96.103 4003 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 20.13 % Favored : 76.46 % 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: 3.11 (0.30), residues: 730 helix: 2.85 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.014 0.002 TYR H 121 ARG 0.003 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.844 Fit side-chains REVERT: A 40 ARG cc_start: 0.8698 (mtp-110) cc_final: 0.8473 (ttm170) REVERT: A 65 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 83 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8214 (mtt90) REVERT: A 129 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7772 (tpt90) REVERT: B 93 GLN cc_start: 0.8333 (mt0) cc_final: 0.7937 (mp10) REVERT: B 95 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7995 (mtp-110) REVERT: C 11 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7289 (pmm-80) REVERT: C 73 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (t160) REVERT: C 91 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: G 73 ASN cc_start: 0.8500 (t0) cc_final: 0.8221 (t0) REVERT: G 91 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.3692 (tp30) outliers start: 21 outliers final: 12 residues processed: 170 average time/residue: 1.9928 time to fit residues: 355.4863 Evaluate side-chains 179 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12645 Z= 0.224 Angle : 0.584 10.003 18321 Z= 0.358 Chirality : 0.035 0.131 2083 Planarity : 0.004 0.031 1316 Dihedral : 30.290 96.153 4003 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.08 % Allowed : 20.13 % Favored : 76.79 % 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: 3.20 (0.31), residues: 730 helix: 2.91 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 194 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 0.011 0.001 TYR H 121 ARG 0.003 0.000 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.867 Fit side-chains REVERT: A 40 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8476 (ttm170) REVERT: A 83 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8224 (mtt90) REVERT: A 129 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7777 (tpt90) REVERT: B 93 GLN cc_start: 0.8312 (mt0) cc_final: 0.7941 (mp10) REVERT: B 95 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7983 (mtp-110) REVERT: C 11 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7308 (pmm-80) REVERT: C 73 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8164 (t160) REVERT: C 91 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: G 73 ASN cc_start: 0.8489 (t0) cc_final: 0.8210 (t0) REVERT: G 91 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.3636 (tp30) outliers start: 19 outliers final: 13 residues processed: 167 average time/residue: 2.0192 time to fit residues: 353.7315 Evaluate side-chains 177 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085248 restraints weight = 18231.240| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.96 r_work: 0.3101 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12645 Z= 0.210 Angle : 0.574 6.469 18321 Z= 0.354 Chirality : 0.035 0.130 2083 Planarity : 0.004 0.030 1316 Dihedral : 30.290 95.998 4003 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.41 % Allowed : 19.97 % Favored : 76.62 % 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: 3.21 (0.31), residues: 730 helix: 2.92 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 194 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 0.012 0.001 TYR F 88 ARG 0.003 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5210.87 seconds wall clock time: 90 minutes 57.97 seconds (5457.97 seconds total)