Starting phenix.real_space_refine on Thu Feb 15 06:17:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfl_33175/02_2024/7xfl_33175_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 267 5.49 5 S 12 5.16 5 C 6343 2.51 5 N 2146 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11425 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2759 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2731 Classifications: {'DNA': 134} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 133} Time building chain proxies: 6.23, per 1000 atoms: 0.55 Number of scatterers: 11425 At special positions: 0 Unit cell: (114.668, 126.24, 79.952, 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 267 15.00 O 2657 8.00 N 2146 7.00 C 6343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 0 sheets defined 64.4% alpha, 0.0% beta 124 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.083A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.314A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.167A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.376A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 342 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for ID residue Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 5.90 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: 2144 1.33 - 1.45: 4115 1.45 - 1.58: 5358 1.58 - 1.70: 533 1.70 - 1.82: 22 Bond restraints: 12172 Sorted by residual: bond pdb=" C3' DI I -53 " pdb=" C4' DI I -53 " ideal model delta sigma weight residual 1.315 1.524 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4' DI I -53 " pdb=" O4' DI I -53 " ideal model delta sigma weight residual 1.640 1.433 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4 DI I -53 " pdb=" N3 DI I -53 " ideal model delta sigma weight residual 1.507 1.354 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C2 DI I -53 " pdb=" N3 DI I -53 " ideal model delta sigma weight residual 1.482 1.344 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C1' DI I -53 " pdb=" O4' DI I -53 " ideal model delta sigma weight residual 1.311 1.429 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 12167 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.89: 1526 105.89 - 113.53: 6823 113.53 - 121.18: 6068 121.18 - 128.83: 3002 128.83 - 136.47: 168 Bond angle restraints: 17587 Sorted by residual: angle pdb=" C1' DI I -53 " pdb=" N9 DI I -53 " pdb=" C4 DI I -53 " ideal model delta sigma weight residual 107.36 124.75 -17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C1' DI I -53 " pdb=" N9 DI I -53 " pdb=" C8 DI I -53 " ideal model delta sigma weight residual 138.51 126.78 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N GLU H 110 " pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " ideal model delta sigma weight residual 110.28 116.32 -6.04 1.55e+00 4.16e-01 1.52e+01 angle pdb=" OP1 DI I -53 " pdb=" P DI I -53 " pdb=" OP2 DI I -53 " ideal model delta sigma weight residual 109.44 119.61 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " ideal model delta sigma weight residual 112.70 122.61 -9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 17582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 5324 35.63 - 71.26: 1280 71.26 - 106.90: 12 106.90 - 142.53: 2 142.53 - 178.16: 1 Dihedral angle restraints: 6619 sinusoidal: 4450 harmonic: 2169 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.16 -178.16 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" C4' DT J 34 " pdb=" C3' DT J 34 " pdb=" O3' DT J 34 " pdb=" P DC J 35 " ideal model delta sinusoidal sigma weight residual 220.00 90.79 129.21 1 3.50e+01 8.16e-04 1.28e+01 ... (remaining 6616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1642 0.054 - 0.109: 309 0.109 - 0.163: 48 0.163 - 0.217: 0 0.217 - 0.272: 4 Chirality restraints: 2003 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' DI I -53 " pdb=" C2' DI I -53 " pdb=" C4' DI I -53 " pdb=" O3' DI I -53 " both_signs ideal model delta sigma weight residual False -2.42 -2.68 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2000 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO G 80 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO C 80 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 50 " 0.017 2.00e-02 2.50e+03 1.72e-02 5.90e+00 pdb=" CG TYR G 50 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR G 50 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR G 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR G 50 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 50 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3666 2.89 - 3.40: 9665 3.40 - 3.90: 22914 3.90 - 4.40: 25987 4.40 - 4.90: 36638 Nonbonded interactions: 98870 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.392 2.520 nonbonded pdb=" OG1 THR A 45 " pdb=" OP1 DC I 70 " model vdw 2.395 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.419 2.440 nonbonded pdb=" O VAL F 60 " pdb=" ND2 ASN F 64 " model vdw 2.433 2.520 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DG I 8 " model vdw 2.447 2.520 ... (remaining 98865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = (chain 'E' and resid 39 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.240 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.420 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.209 12172 Z= 0.404 Angle : 0.750 17.386 17587 Z= 0.431 Chirality : 0.044 0.272 2003 Planarity : 0.007 0.069 1299 Dihedral : 27.327 178.160 5221 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 733 helix: -0.39 (0.19), residues: 540 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE F 61 TYR 0.040 0.002 TYR G 50 ARG 0.014 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.843 Fit side-chains REVERT: A 90 MET cc_start: 0.6844 (mmp) cc_final: 0.6421 (mmp) REVERT: B 31 LYS cc_start: 0.8214 (tttp) cc_final: 0.7990 (tttp) REVERT: D 39 TYR cc_start: 0.7589 (t80) cc_final: 0.7337 (t80) REVERT: D 87 THR cc_start: 0.8500 (p) cc_final: 0.8250 (p) REVERT: D 92 GLN cc_start: 0.8289 (tt0) cc_final: 0.8030 (tt0) REVERT: F 44 LYS cc_start: 0.8003 (tttt) cc_final: 0.7621 (tttp) REVERT: F 78 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7937 (mtm110) REVERT: G 57 TYR cc_start: 0.8534 (t80) cc_final: 0.8116 (t80) REVERT: G 77 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7259 (mtt90) REVERT: H 33 SER cc_start: 0.8892 (p) cc_final: 0.8644 (p) REVERT: H 40 LYS cc_start: 0.8262 (mttm) cc_final: 0.8060 (mttt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 2.0946 time to fit residues: 348.6112 Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN E 68 GLN E 76 GLN F 27 GLN F 64 ASN G 24 GLN G 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12172 Z= 0.201 Angle : 0.538 6.563 17587 Z= 0.324 Chirality : 0.033 0.134 2003 Planarity : 0.005 0.049 1299 Dihedral : 30.385 179.271 3748 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.09 % Allowed : 10.77 % Favored : 87.14 % 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: 1.11 (0.29), residues: 733 helix: 1.30 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.008 0.002 PHE E 67 TYR 0.012 0.002 TYR G 57 ARG 0.004 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.870 Fit side-chains REVERT: A 90 MET cc_start: 0.6991 (mmp) cc_final: 0.6705 (mmp) REVERT: A 129 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7119 (ttp80) REVERT: B 49 LEU cc_start: 0.8731 (mt) cc_final: 0.8450 (mt) REVERT: B 63 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 92 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7797 (mmm160) REVERT: C 104 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7300 (mm110) REVERT: D 39 TYR cc_start: 0.7675 (t80) cc_final: 0.7397 (t80) REVERT: E 59 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: E 79 LYS cc_start: 0.8122 (tttp) cc_final: 0.7900 (tttp) REVERT: F 44 LYS cc_start: 0.7970 (tttt) cc_final: 0.7747 (tttp) REVERT: F 59 LYS cc_start: 0.7562 (tttp) cc_final: 0.7178 (ttmm) REVERT: G 57 TYR cc_start: 0.8655 (t80) cc_final: 0.8355 (t80) REVERT: H 40 LYS cc_start: 0.8225 (mttm) cc_final: 0.8011 (mtpt) outliers start: 13 outliers final: 4 residues processed: 129 average time/residue: 1.9247 time to fit residues: 261.0870 Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 113 HIS D 60 ASN D 79 HIS E 76 GLN F 25 ASN F 27 GLN G 24 GLN G 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12172 Z= 0.172 Angle : 0.517 6.249 17587 Z= 0.315 Chirality : 0.033 0.126 2003 Planarity : 0.004 0.043 1299 Dihedral : 30.386 178.830 3748 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.61 % Allowed : 13.50 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.30), residues: 733 helix: 1.87 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.001 TYR F 88 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.821 Fit side-chains REVERT: A 52 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.7152 (mpp-170) REVERT: A 90 MET cc_start: 0.6992 (mmp) cc_final: 0.6731 (mmp) REVERT: B 49 LEU cc_start: 0.8734 (mt) cc_final: 0.8454 (mt) REVERT: B 63 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 92 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7788 (mmm160) REVERT: C 77 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7417 (ttp-110) REVERT: C 104 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7288 (mm-40) REVERT: D 39 TYR cc_start: 0.7629 (t80) cc_final: 0.7395 (t80) REVERT: E 59 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: E 79 LYS cc_start: 0.8114 (tttp) cc_final: 0.7894 (tttp) REVERT: F 44 LYS cc_start: 0.7984 (tttt) cc_final: 0.7760 (tttp) REVERT: F 59 LYS cc_start: 0.7543 (tttp) cc_final: 0.7221 (tttm) REVERT: G 41 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: H 40 LYS cc_start: 0.8171 (mttm) cc_final: 0.7883 (mtmt) REVERT: H 82 LYS cc_start: 0.7857 (mptp) cc_final: 0.7481 (mptp) outliers start: 10 outliers final: 1 residues processed: 115 average time/residue: 2.1058 time to fit residues: 253.6559 Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 93 GLN D 60 ASN D 79 HIS E 76 GLN F 27 GLN G 24 GLN G 73 ASN H 79 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12172 Z= 0.328 Angle : 0.618 6.557 17587 Z= 0.364 Chirality : 0.039 0.147 2003 Planarity : 0.005 0.042 1299 Dihedral : 30.887 179.263 3748 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.22 % Allowed : 13.34 % Favored : 83.44 % 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: 733 helix: 1.73 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 106 PHE 0.014 0.002 PHE B 100 TYR 0.016 0.002 TYR F 88 ARG 0.008 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.833 Fit side-chains REVERT: A 42 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6969 (mtt180) REVERT: A 50 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 90 MET cc_start: 0.7051 (mmp) cc_final: 0.6750 (mmp) REVERT: A 122 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (ptpp) REVERT: A 129 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7103 (ttp80) REVERT: B 49 LEU cc_start: 0.8762 (mt) cc_final: 0.8497 (mt) REVERT: B 63 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 71 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.6784 (ttp80) REVERT: C 77 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7499 (ttp-110) REVERT: D 36 ILE cc_start: 0.8263 (tt) cc_final: 0.7838 (tp) REVERT: D 39 TYR cc_start: 0.7659 (t80) cc_final: 0.7427 (t80) REVERT: D 105 LYS cc_start: 0.7454 (mttt) cc_final: 0.6925 (mmtt) REVERT: E 56 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8034 (ptpp) REVERT: E 59 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6104 (pm20) REVERT: E 86 SER cc_start: 0.8165 (p) cc_final: 0.7958 (m) REVERT: F 59 LYS cc_start: 0.7528 (tttp) cc_final: 0.7176 (ttmm) REVERT: F 92 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7334 (mtp85) REVERT: G 41 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: H 48 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6461 (m-30) REVERT: H 53 SER cc_start: 0.8148 (t) cc_final: 0.7715 (p) REVERT: H 82 LYS cc_start: 0.7973 (mptp) cc_final: 0.7599 (mptp) REVERT: H 113 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7962 (ttpt) outliers start: 20 outliers final: 5 residues processed: 125 average time/residue: 2.1046 time to fit residues: 275.5157 Evaluate side-chains 122 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0020 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 79 HIS D 106 HIS E 125 GLN F 27 GLN F 75 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12172 Z= 0.174 Angle : 0.559 6.259 17587 Z= 0.338 Chirality : 0.034 0.133 2003 Planarity : 0.004 0.037 1299 Dihedral : 30.865 179.574 3748 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.41 % Allowed : 15.27 % Favored : 82.32 % 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: 2.04 (0.30), residues: 733 helix: 2.07 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 79 PHE 0.011 0.001 PHE H 62 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.858 Fit side-chains REVERT: A 90 MET cc_start: 0.7021 (mmp) cc_final: 0.6716 (mmp) REVERT: A 122 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7849 (ptpp) REVERT: A 129 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7098 (ttp80) REVERT: B 63 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 61 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: C 71 ARG cc_start: 0.7015 (ttp-170) cc_final: 0.6787 (ttp80) REVERT: D 39 TYR cc_start: 0.7609 (t80) cc_final: 0.7393 (t80) REVERT: E 59 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: E 86 SER cc_start: 0.8077 (p) cc_final: 0.7867 (m) REVERT: F 59 LYS cc_start: 0.7473 (tttp) cc_final: 0.7145 (ttmm) REVERT: H 48 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: H 82 LYS cc_start: 0.7970 (mptp) cc_final: 0.7561 (mppt) REVERT: H 113 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7939 (ttpt) outliers start: 15 outliers final: 2 residues processed: 112 average time/residue: 2.2587 time to fit residues: 264.5397 Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 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 76 GLN B 93 GLN D 79 HIS E 125 GLN F 27 GLN G 24 GLN H 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12172 Z= 0.343 Angle : 0.633 6.582 17587 Z= 0.372 Chirality : 0.040 0.149 2003 Planarity : 0.005 0.042 1299 Dihedral : 31.007 177.320 3748 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.22 % Allowed : 14.31 % Favored : 82.48 % 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: 1.70 (0.30), residues: 733 helix: 1.81 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 106 PHE 0.014 0.002 PHE B 100 TYR 0.016 0.002 TYR C 57 ARG 0.007 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.945 Fit side-chains REVERT: A 50 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 65 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 90 MET cc_start: 0.7009 (mmp) cc_final: 0.6631 (mmp) REVERT: A 122 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (ptpp) REVERT: A 129 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7144 (ttp80) REVERT: B 63 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 71 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6745 (ttp80) REVERT: D 105 LYS cc_start: 0.7348 (mttt) cc_final: 0.6404 (ttpp) REVERT: E 59 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.5992 (pm20) REVERT: F 59 LYS cc_start: 0.7573 (tttp) cc_final: 0.7273 (ttmm) REVERT: G 41 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: H 82 LYS cc_start: 0.7918 (mptp) cc_final: 0.7688 (mppt) outliers start: 20 outliers final: 7 residues processed: 113 average time/residue: 2.0415 time to fit residues: 242.1174 Evaluate side-chains 111 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN D 79 HIS E 125 GLN F 27 GLN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12172 Z= 0.178 Angle : 0.575 6.470 17587 Z= 0.347 Chirality : 0.035 0.134 2003 Planarity : 0.004 0.038 1299 Dihedral : 30.986 178.018 3748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.25 % Allowed : 15.43 % Favored : 82.32 % 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 (0.30), residues: 733 helix: 2.10 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR F 51 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.035 Fit side-chains REVERT: A 90 MET cc_start: 0.6995 (mmp) cc_final: 0.6626 (mmp) REVERT: A 122 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7883 (ptpp) REVERT: A 129 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7138 (ttp80) REVERT: B 63 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 71 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6748 (ttp80) REVERT: E 59 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.5884 (pm20) REVERT: F 59 LYS cc_start: 0.7480 (tttp) cc_final: 0.7182 (ttmm) REVERT: F 92 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7325 (mtp85) REVERT: H 48 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: H 82 LYS cc_start: 0.7893 (mptp) cc_final: 0.7485 (mptp) outliers start: 14 outliers final: 4 residues processed: 105 average time/residue: 2.0003 time to fit residues: 220.5745 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN D 79 HIS E 125 GLN F 27 GLN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12172 Z= 0.219 Angle : 0.573 6.152 17587 Z= 0.344 Chirality : 0.036 0.131 2003 Planarity : 0.004 0.039 1299 Dihedral : 30.946 178.920 3748 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.73 % Allowed : 15.43 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.30), residues: 733 helix: 2.11 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.71 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.010 0.002 PHE E 67 TYR 0.013 0.002 TYR F 51 ARG 0.005 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.869 Fit side-chains REVERT: A 50 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 65 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 90 MET cc_start: 0.7068 (mmp) cc_final: 0.6696 (mmp) REVERT: A 122 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7946 (ptpp) REVERT: A 129 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7150 (ttp80) REVERT: B 63 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 71 ARG cc_start: 0.7155 (ttp-170) cc_final: 0.6733 (ttp80) REVERT: E 59 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: E 65 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8295 (mm) REVERT: F 59 LYS cc_start: 0.7501 (tttp) cc_final: 0.7197 (ttmm) REVERT: H 48 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: H 82 LYS cc_start: 0.7891 (mptp) cc_final: 0.7687 (mppt) outliers start: 17 outliers final: 5 residues processed: 106 average time/residue: 2.0391 time to fit residues: 226.9367 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN D 79 HIS E 39 HIS E 125 GLN F 27 GLN H 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12172 Z= 0.310 Angle : 0.609 6.283 17587 Z= 0.360 Chirality : 0.039 0.148 2003 Planarity : 0.005 0.041 1299 Dihedral : 30.948 178.598 3748 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.41 % Allowed : 15.59 % Favored : 81.99 % 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: 1.83 (0.30), residues: 733 helix: 1.92 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 106 PHE 0.011 0.002 PHE B 100 TYR 0.015 0.002 TYR C 57 ARG 0.005 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.961 Fit side-chains REVERT: A 50 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 65 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 90 MET cc_start: 0.7052 (mmp) cc_final: 0.6681 (mmp) REVERT: A 122 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.8002 (ptpp) REVERT: A 129 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7141 (ttp80) REVERT: B 63 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7534 (mt-10) REVERT: C 71 ARG cc_start: 0.7156 (ttp-170) cc_final: 0.6737 (ttp80) REVERT: D 105 LYS cc_start: 0.7334 (mttt) cc_final: 0.6890 (mmtt) REVERT: E 59 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.5986 (pm20) REVERT: E 65 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (mm) REVERT: F 59 LYS cc_start: 0.7575 (tttp) cc_final: 0.7275 (ttmm) REVERT: G 41 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: H 48 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6510 (m-30) REVERT: H 82 LYS cc_start: 0.7903 (mptp) cc_final: 0.7673 (mppt) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 2.0563 time to fit residues: 230.8842 Evaluate side-chains 111 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU 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: 0.5980 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 79 HIS E 125 GLN F 27 GLN G 24 GLN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12172 Z= 0.194 Angle : 0.580 6.208 17587 Z= 0.348 Chirality : 0.035 0.134 2003 Planarity : 0.004 0.039 1299 Dihedral : 30.940 178.451 3748 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.09 % Allowed : 16.08 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.30), residues: 733 helix: 2.03 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.010 0.002 PHE B 100 TYR 0.012 0.002 TYR F 51 ARG 0.004 0.001 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.880 Fit side-chains REVERT: A 50 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 65 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7738 (tp) REVERT: A 90 MET cc_start: 0.7083 (mmp) cc_final: 0.6711 (mmp) REVERT: A 122 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7921 (ptpp) REVERT: A 129 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7132 (ttp80) REVERT: B 63 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 71 ARG cc_start: 0.7165 (ttp-170) cc_final: 0.6803 (ttp80) REVERT: E 59 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.5971 (pm20) REVERT: E 65 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8253 (mm) REVERT: F 59 LYS cc_start: 0.7550 (tttp) cc_final: 0.7259 (ttmm) REVERT: G 41 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: H 48 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: H 82 LYS cc_start: 0.7907 (mptp) cc_final: 0.7676 (mppt) outliers start: 13 outliers final: 5 residues processed: 105 average time/residue: 2.1393 time to fit residues: 235.4359 Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU 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: 1.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 93 GLN D 79 HIS D 81 ASN E 125 GLN F 27 GLN G 24 GLN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123981 restraints weight = 11309.197| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 0.78 r_work: 0.3200 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12172 Z= 0.236 Angle : 0.580 6.224 17587 Z= 0.347 Chirality : 0.036 0.135 2003 Planarity : 0.004 0.039 1299 Dihedral : 30.938 178.814 3748 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.25 % Allowed : 16.08 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.30), residues: 733 helix: 2.04 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.009 0.002 PHE E 67 TYR 0.012 0.002 TYR F 51 ARG 0.004 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4162.94 seconds wall clock time: 74 minutes 19.35 seconds (4459.35 seconds total)