Starting phenix.real_space_refine on Fri Mar 15 08:13:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/03_2024/7n8n_24238.pdb" } resolution = 3.89 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= 0.002 sd= 0.018 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 248 5.49 5 S 30 5.16 5 C 6180 2.51 5 N 2053 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2543 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2576 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Time building chain proxies: 6.16, per 1000 atoms: 0.55 Number of scatterers: 11121 At special positions: 0 Unit cell: (86.265, 111.825, 116.085, 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 30 16.00 P 248 15.00 O 2610 8.00 N 2053 7.00 C 6180 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: 7.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 67.4% alpha, 0.5% beta 124 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.561A pdb=" N VAL A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.975A pdb=" N GLN A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 172 through 201 Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.885A pdb=" N GLU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.562A pdb=" N VAL C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.976A pdb=" N GLN C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 172 through 201 Processing helix chain 'C' and resid 207 through 219 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 4.884A pdb=" N GLU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 205 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 7.54 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: 2475 1.33 - 1.45: 3579 1.45 - 1.57: 5210 1.57 - 1.69: 496 1.69 - 1.81: 52 Bond restraints: 11812 Sorted by residual: bond pdb=" CZ ARG B 157 " pdb=" NH2 ARG B 157 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.01e+00 bond pdb=" CZ ARG D 157 " pdb=" NH2 ARG D 157 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CA VAL A 56 " pdb=" CB VAL A 56 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.77e+00 bond pdb=" CA VAL C 56 " pdb=" CB VAL C 56 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.30e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 11807 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.25: 931 104.25 - 111.35: 6057 111.35 - 118.45: 3564 118.45 - 125.55: 5631 125.55 - 132.65: 814 Bond angle restraints: 16997 Sorted by residual: angle pdb=" CB MET C 157 " pdb=" CG MET C 157 " pdb=" SD MET C 157 " ideal model delta sigma weight residual 112.70 102.55 10.15 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 102.57 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA LEU B 166 " pdb=" CB LEU B 166 " pdb=" CG LEU B 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" CA LEU D 166 " pdb=" CB LEU D 166 " pdb=" CG LEU D 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C4 DT I -64 " pdb=" C5 DT I -64 " pdb=" C7 DT I -64 " ideal model delta sigma weight residual 122.40 117.59 4.81 1.50e+00 4.44e-01 1.03e+01 ... (remaining 16992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5236 34.91 - 69.81: 1210 69.81 - 104.72: 17 104.72 - 139.63: 2 139.63 - 174.54: 3 Dihedral angle restraints: 6468 sinusoidal: 4198 harmonic: 2270 Sorted by residual: dihedral pdb=" CA SER C 131 " pdb=" C SER C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta harmonic sigma weight residual -180.00 -63.39 -116.61 0 5.00e+00 4.00e-02 5.44e+02 dihedral pdb=" CA SER A 131 " pdb=" C SER A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual -180.00 -63.45 -116.55 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" N GLY C 113 " pdb=" CA GLY C 113 " ideal model delta harmonic sigma weight residual -180.00 -99.23 -80.77 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1311 0.036 - 0.072: 474 0.072 - 0.108: 133 0.108 - 0.143: 39 0.143 - 0.179: 7 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CG LEU C 41 " pdb=" CB LEU C 41 " pdb=" CD1 LEU C 41 " pdb=" CD2 LEU C 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1961 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 135 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C LYS B 135 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS B 135 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 136 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 135 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LYS D 135 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS D 135 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 136 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 65 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" CG ASN D 65 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 65 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 65 " -0.016 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 246 2.61 - 3.18: 10949 3.18 - 3.75: 22515 3.75 - 4.33: 27845 4.33 - 4.90: 37785 Nonbonded interactions: 99340 Sorted by model distance: nonbonded pdb=" O GLU A 132 " pdb=" OG SER A 135 " model vdw 2.035 2.440 nonbonded pdb=" O GLU C 132 " pdb=" OG SER C 135 " model vdw 2.036 2.440 nonbonded pdb=" OG SER A 185 " pdb=" O GLY D 219 " model vdw 2.101 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 38 " model vdw 2.103 2.440 nonbonded pdb=" O LYS C 35 " pdb=" OG1 THR C 38 " model vdw 2.104 2.440 ... (remaining 99335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 4.080 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.410 Find NCS groups from input model: 0.430 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.006 0.045 11812 Z= 0.360 Angle : 0.849 11.271 16997 Z= 0.504 Chirality : 0.042 0.179 1964 Planarity : 0.006 0.054 1276 Dihedral : 27.929 174.537 5000 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.71 (0.28), residues: 790 helix: -0.13 (0.22), residues: 484 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS C 219 PHE 0.024 0.004 PHE C 154 TYR 0.020 0.002 TYR D 121 ARG 0.007 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8660 (m-80) cc_final: 0.8387 (m-80) REVERT: A 71 GLN cc_start: 0.9698 (mt0) cc_final: 0.9420 (mt0) REVERT: A 216 MET cc_start: 0.9220 (tpt) cc_final: 0.9011 (tpt) REVERT: B 45 MET cc_start: 0.8391 (mmm) cc_final: 0.8031 (mmm) REVERT: B 121 TYR cc_start: 0.9022 (t80) cc_final: 0.8629 (t80) REVERT: B 166 LEU cc_start: 0.9596 (tp) cc_final: 0.9356 (tp) REVERT: B 187 ASP cc_start: 0.9258 (m-30) cc_final: 0.9057 (m-30) REVERT: C 69 LEU cc_start: 0.9641 (mm) cc_final: 0.9422 (mm) REVERT: C 71 GLN cc_start: 0.9440 (mt0) cc_final: 0.9211 (mm-40) REVERT: C 77 MET cc_start: 0.9414 (ppp) cc_final: 0.9130 (ppp) REVERT: C 83 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9191 (ptmt) REVERT: C 157 MET cc_start: 0.9086 (mtt) cc_final: 0.8543 (mmm) REVERT: C 177 ASP cc_start: 0.9514 (m-30) cc_final: 0.9240 (p0) REVERT: C 199 TYR cc_start: 0.9337 (m-10) cc_final: 0.9093 (m-80) REVERT: C 216 MET cc_start: 0.8803 (tpt) cc_final: 0.8269 (tpp) REVERT: D 108 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8270 (ttp80) REVERT: D 174 MET cc_start: 0.9714 (mmp) cc_final: 0.9334 (mmp) REVERT: D 176 GLU cc_start: 0.9412 (tt0) cc_final: 0.9143 (tm-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2132 time to fit residues: 54.5112 Evaluate side-chains 115 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11812 Z= 0.233 Angle : 0.725 10.129 16997 Z= 0.413 Chirality : 0.041 0.255 1964 Planarity : 0.006 0.067 1276 Dihedral : 30.927 173.457 3544 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 4.02 % Allowed : 10.99 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.10 (0.29), residues: 790 helix: 0.23 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 167 PHE 0.013 0.002 PHE A 61 TYR 0.022 0.002 TYR B 172 ARG 0.006 0.001 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8604 (m-80) cc_final: 0.8315 (m-80) REVERT: A 142 MET cc_start: 0.8973 (ptm) cc_final: 0.8694 (ptp) REVERT: B 45 MET cc_start: 0.8604 (mmm) cc_final: 0.8280 (mmm) REVERT: B 121 TYR cc_start: 0.8970 (t80) cc_final: 0.8388 (t80) REVERT: B 149 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9357 (mm) REVERT: B 166 LEU cc_start: 0.9533 (tp) cc_final: 0.9264 (tp) REVERT: C 64 MET cc_start: 0.8620 (mmt) cc_final: 0.8309 (mmt) REVERT: C 71 GLN cc_start: 0.9399 (mt0) cc_final: 0.9123 (mm-40) REVERT: C 77 MET cc_start: 0.9335 (ppp) cc_final: 0.8994 (ppp) REVERT: C 116 PHE cc_start: 0.7279 (t80) cc_final: 0.6924 (t80) REVERT: C 199 TYR cc_start: 0.9284 (m-10) cc_final: 0.8837 (m-80) REVERT: C 216 MET cc_start: 0.8818 (tpt) cc_final: 0.8270 (tpp) REVERT: D 69 PHE cc_start: 0.9291 (t80) cc_final: 0.9087 (t80) REVERT: D 108 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8263 (ttp80) REVERT: D 174 MET cc_start: 0.9649 (mmp) cc_final: 0.9351 (mmp) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.2133 time to fit residues: 45.2466 Evaluate side-chains 138 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 65 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11812 Z= 0.327 Angle : 0.725 8.152 16997 Z= 0.422 Chirality : 0.040 0.165 1964 Planarity : 0.006 0.072 1276 Dihedral : 30.899 175.364 3544 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.11 % Favored : 90.63 % Rotamer: Outliers : 4.02 % Allowed : 15.94 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.16 (0.28), residues: 790 helix: 0.20 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.59 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 40 PHE 0.014 0.002 PHE D 209 TYR 0.015 0.002 TYR B 121 ARG 0.005 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8551 (m-80) cc_final: 0.8221 (m-80) REVERT: A 71 GLN cc_start: 0.9657 (mt0) cc_final: 0.9442 (mt0) REVERT: A 142 MET cc_start: 0.8981 (ptm) cc_final: 0.8711 (ppp) REVERT: A 177 ASP cc_start: 0.9147 (m-30) cc_final: 0.8931 (m-30) REVERT: B 45 MET cc_start: 0.8594 (mmm) cc_final: 0.8364 (mmm) REVERT: B 121 TYR cc_start: 0.9032 (t80) cc_final: 0.8529 (t80) REVERT: B 166 LEU cc_start: 0.9525 (tp) cc_final: 0.9309 (tp) REVERT: C 64 MET cc_start: 0.8789 (mmt) cc_final: 0.8184 (mmt) REVERT: C 71 GLN cc_start: 0.9473 (mt0) cc_final: 0.9244 (mt0) REVERT: C 77 MET cc_start: 0.9429 (ppp) cc_final: 0.8953 (ppp) REVERT: C 139 ARG cc_start: 0.8654 (mmm160) cc_final: 0.7913 (mpt-90) REVERT: C 180 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8785 (mm-40) REVERT: C 199 TYR cc_start: 0.9394 (m-10) cc_final: 0.9155 (m-80) REVERT: C 216 MET cc_start: 0.8856 (tpt) cc_final: 0.8343 (tpp) REVERT: D 108 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8425 (ttp80) outliers start: 26 outliers final: 15 residues processed: 137 average time/residue: 0.2077 time to fit residues: 41.4970 Evaluate side-chains 126 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 26 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11812 Z= 0.216 Angle : 0.685 8.853 16997 Z= 0.391 Chirality : 0.039 0.241 1964 Planarity : 0.005 0.073 1276 Dihedral : 30.844 175.483 3544 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.96 % Favored : 92.78 % Rotamer: Outliers : 2.63 % Allowed : 18.11 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.82 (0.29), residues: 790 helix: 0.47 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 109 PHE 0.024 0.002 PHE D 173 TYR 0.015 0.002 TYR B 172 ARG 0.005 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8375 (m-80) cc_final: 0.7992 (m-80) REVERT: A 71 GLN cc_start: 0.9656 (mt0) cc_final: 0.9437 (mt0) REVERT: A 95 GLU cc_start: 0.9242 (pp20) cc_final: 0.8745 (tp30) REVERT: A 142 MET cc_start: 0.9106 (ptm) cc_final: 0.8817 (ppp) REVERT: B 121 TYR cc_start: 0.9035 (t80) cc_final: 0.8511 (t80) REVERT: B 170 ILE cc_start: 0.9501 (tt) cc_final: 0.9301 (tp) REVERT: B 174 MET cc_start: 0.9506 (mmp) cc_final: 0.9273 (mmm) REVERT: C 64 MET cc_start: 0.8636 (mmt) cc_final: 0.8010 (mmt) REVERT: C 77 MET cc_start: 0.9437 (ppp) cc_final: 0.9017 (ppp) REVERT: C 180 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8772 (mm110) REVERT: C 216 MET cc_start: 0.8829 (tpt) cc_final: 0.8292 (tpp) REVERT: D 108 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8423 (ttp80) REVERT: D 174 MET cc_start: 0.9666 (mmp) cc_final: 0.9327 (mmp) REVERT: D 217 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (p90) outliers start: 17 outliers final: 10 residues processed: 139 average time/residue: 0.2221 time to fit residues: 44.2434 Evaluate side-chains 124 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11812 Z= 0.318 Angle : 0.708 9.207 16997 Z= 0.412 Chirality : 0.040 0.210 1964 Planarity : 0.006 0.074 1276 Dihedral : 30.978 177.157 3544 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 4.49 % Allowed : 20.12 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.94 (0.29), residues: 790 helix: 0.38 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.50 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 167 PHE 0.043 0.004 PHE C 116 TYR 0.024 0.003 TYR B 172 ARG 0.008 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8379 (m-80) cc_final: 0.8023 (m-80) REVERT: A 86 MET cc_start: 0.7892 (mtt) cc_final: 0.7375 (mmm) REVERT: A 95 GLU cc_start: 0.9291 (pp20) cc_final: 0.8982 (tp30) REVERT: A 142 MET cc_start: 0.9029 (ptm) cc_final: 0.8708 (ppp) REVERT: A 212 GLU cc_start: 0.9470 (mp0) cc_final: 0.9215 (mp0) REVERT: B 109 HIS cc_start: 0.9199 (t70) cc_final: 0.8451 (t-90) REVERT: B 121 TYR cc_start: 0.9072 (t80) cc_final: 0.8556 (t80) REVERT: C 64 MET cc_start: 0.8676 (mmt) cc_final: 0.7953 (mmt) REVERT: C 77 MET cc_start: 0.9462 (ppp) cc_final: 0.9152 (ppp) REVERT: C 216 MET cc_start: 0.8837 (tpt) cc_final: 0.8325 (tpp) REVERT: D 108 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8573 (ttp80) REVERT: D 174 MET cc_start: 0.9693 (mmp) cc_final: 0.9491 (mmp) outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 0.2127 time to fit residues: 41.7017 Evaluate side-chains 130 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11812 Z= 0.252 Angle : 0.691 14.170 16997 Z= 0.397 Chirality : 0.038 0.157 1964 Planarity : 0.005 0.073 1276 Dihedral : 31.056 178.845 3544 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.09 % Favored : 92.66 % Rotamer: Outliers : 2.94 % Allowed : 22.76 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.29), residues: 790 helix: 0.55 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 167 PHE 0.011 0.002 PHE A 154 TYR 0.018 0.002 TYR B 172 ARG 0.007 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8332 (m-80) cc_final: 0.7985 (m-80) REVERT: A 95 GLU cc_start: 0.9270 (pp20) cc_final: 0.8933 (tp30) REVERT: A 142 MET cc_start: 0.8968 (ptm) cc_final: 0.8702 (ppp) REVERT: A 212 GLU cc_start: 0.9435 (mp0) cc_final: 0.9153 (mp0) REVERT: B 109 HIS cc_start: 0.9254 (t70) cc_final: 0.8495 (t-90) REVERT: B 121 TYR cc_start: 0.9063 (t80) cc_final: 0.8599 (t80) REVERT: B 170 ILE cc_start: 0.9530 (tt) cc_final: 0.9189 (tp) REVERT: B 174 MET cc_start: 0.9479 (mmm) cc_final: 0.8885 (mmm) REVERT: C 64 MET cc_start: 0.8700 (mmt) cc_final: 0.8025 (mmt) REVERT: C 77 MET cc_start: 0.9462 (ppp) cc_final: 0.9098 (ppp) REVERT: C 216 MET cc_start: 0.8822 (tpt) cc_final: 0.8293 (tpp) REVERT: D 174 MET cc_start: 0.9672 (mmp) cc_final: 0.9441 (mmp) outliers start: 19 outliers final: 16 residues processed: 131 average time/residue: 0.2113 time to fit residues: 40.2199 Evaluate side-chains 130 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11812 Z= 0.248 Angle : 0.692 11.985 16997 Z= 0.395 Chirality : 0.039 0.171 1964 Planarity : 0.005 0.072 1276 Dihedral : 31.093 179.249 3544 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.34 % Favored : 92.41 % Rotamer: Outliers : 3.10 % Allowed : 26.47 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.29), residues: 790 helix: 0.64 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.42 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 167 PHE 0.014 0.002 PHE B 209 TYR 0.018 0.002 TYR B 172 ARG 0.006 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8345 (m-10) cc_final: 0.7928 (m-80) REVERT: A 95 GLU cc_start: 0.9232 (pp20) cc_final: 0.8947 (tp30) REVERT: A 142 MET cc_start: 0.8988 (ptm) cc_final: 0.8711 (ppp) REVERT: B 45 MET cc_start: 0.8351 (mmm) cc_final: 0.7982 (mmm) REVERT: B 109 HIS cc_start: 0.9072 (t-90) cc_final: 0.8621 (t70) REVERT: B 121 TYR cc_start: 0.9015 (t80) cc_final: 0.8666 (t80) REVERT: C 64 MET cc_start: 0.8683 (mmt) cc_final: 0.8112 (mmt) REVERT: C 77 MET cc_start: 0.9471 (ppp) cc_final: 0.8995 (ppp) REVERT: C 216 MET cc_start: 0.8790 (tpt) cc_final: 0.8259 (tpp) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.1728 time to fit residues: 32.1831 Evaluate side-chains 118 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11812 Z= 0.280 Angle : 0.709 12.114 16997 Z= 0.406 Chirality : 0.039 0.223 1964 Planarity : 0.006 0.099 1276 Dihedral : 31.181 179.467 3544 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.97 % Favored : 91.77 % Rotamer: Outliers : 2.94 % Allowed : 27.24 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.70 (0.29), residues: 790 helix: 0.58 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.40 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 167 PHE 0.016 0.002 PHE A 215 TYR 0.016 0.002 TYR B 172 ARG 0.024 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8392 (m-10) cc_final: 0.7966 (m-80) REVERT: A 77 MET cc_start: 0.9513 (tmm) cc_final: 0.9298 (tmm) REVERT: A 95 GLU cc_start: 0.9218 (pp20) cc_final: 0.8973 (tp30) REVERT: A 142 MET cc_start: 0.9027 (ptm) cc_final: 0.8754 (ppp) REVERT: B 121 TYR cc_start: 0.9033 (t80) cc_final: 0.8678 (t80) REVERT: B 174 MET cc_start: 0.9438 (mmm) cc_final: 0.9068 (mmm) REVERT: C 64 MET cc_start: 0.8700 (mmt) cc_final: 0.8148 (mmt) REVERT: C 77 MET cc_start: 0.9509 (ppp) cc_final: 0.9035 (ppp) REVERT: C 216 MET cc_start: 0.8785 (tpt) cc_final: 0.8302 (tpp) outliers start: 19 outliers final: 17 residues processed: 120 average time/residue: 0.2040 time to fit residues: 36.3945 Evaluate side-chains 121 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11812 Z= 0.350 Angle : 0.762 11.417 16997 Z= 0.437 Chirality : 0.042 0.203 1964 Planarity : 0.006 0.079 1276 Dihedral : 31.498 176.845 3544 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.37 % Favored : 90.38 % Rotamer: Outliers : 3.10 % Allowed : 27.40 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.97 (0.29), residues: 790 helix: 0.33 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -2.50 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 197 PHE 0.015 0.002 PHE D 38 TYR 0.021 0.003 TYR B 172 ARG 0.023 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8497 (m-10) cc_final: 0.7572 (m-80) REVERT: A 77 MET cc_start: 0.9548 (tmm) cc_final: 0.9329 (tmm) REVERT: A 95 GLU cc_start: 0.9207 (pp20) cc_final: 0.8986 (tp30) REVERT: A 142 MET cc_start: 0.9087 (ptm) cc_final: 0.8796 (ppp) REVERT: B 45 MET cc_start: 0.8252 (mmm) cc_final: 0.7966 (mmm) REVERT: C 64 MET cc_start: 0.8843 (mmt) cc_final: 0.8291 (mmt) REVERT: C 77 MET cc_start: 0.9471 (ppp) cc_final: 0.8888 (ppp) REVERT: C 180 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8913 (mm-40) REVERT: C 216 MET cc_start: 0.8733 (tpt) cc_final: 0.8254 (tpp) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.2158 time to fit residues: 37.5904 Evaluate side-chains 121 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 50.0000 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11812 Z= 0.330 Angle : 0.758 11.252 16997 Z= 0.434 Chirality : 0.041 0.210 1964 Planarity : 0.006 0.095 1276 Dihedral : 31.602 174.985 3544 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.85 % Favored : 91.90 % Rotamer: Outliers : 2.79 % Allowed : 28.02 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.29), residues: 790 helix: 0.27 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 109 PHE 0.015 0.002 PHE B 38 TYR 0.025 0.003 TYR B 172 ARG 0.020 0.001 ARG C 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8507 (m-10) cc_final: 0.7527 (m-80) REVERT: A 77 MET cc_start: 0.9553 (tmm) cc_final: 0.9328 (tmm) REVERT: A 142 MET cc_start: 0.9184 (ptm) cc_final: 0.8904 (ppp) REVERT: B 43 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.9066 (mmm160) REVERT: B 45 MET cc_start: 0.8266 (mmm) cc_final: 0.7999 (mmm) REVERT: C 64 MET cc_start: 0.8833 (mmt) cc_final: 0.8287 (mmt) REVERT: C 77 MET cc_start: 0.9478 (ppp) cc_final: 0.8892 (ppp) REVERT: C 180 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8836 (mm-40) REVERT: C 216 MET cc_start: 0.8726 (tpt) cc_final: 0.8502 (tpt) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.2222 time to fit residues: 38.4630 Evaluate side-chains 120 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.061541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.045741 restraints weight = 69318.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047315 restraints weight = 41647.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048410 restraints weight = 29568.220| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11812 Z= 0.218 Angle : 0.722 11.600 16997 Z= 0.407 Chirality : 0.039 0.213 1964 Planarity : 0.006 0.087 1276 Dihedral : 31.371 175.232 3544 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Rotamer: Outliers : 2.63 % Allowed : 28.64 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.72 (0.30), residues: 790 helix: 0.57 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.43 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 40 PHE 0.019 0.002 PHE A 215 TYR 0.018 0.002 TYR B 172 ARG 0.019 0.001 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.30 seconds wall clock time: 35 minutes 26.35 seconds (2126.35 seconds total)