Starting phenix.real_space_refine on Tue Feb 13 12:03:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrx_34981/02_2024/8hrx_34981.pdb" } resolution = 2.89 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3872 2.51 5 N 973 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 16": "OD1" <-> "OD2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L PHE 209": "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: 6013 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2322 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 7, 'TRANS': 39} Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1661 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1659 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Time building chain proxies: 3.85, per 1000 atoms: 0.64 Number of scatterers: 6013 At special positions: 0 Unit cell: (74.7, 68.06, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1125 8.00 N 973 7.00 C 3872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 34.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.906A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 Proline residue: A 135 - end of helix removed outlier: 3.891A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.603A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.604A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.150A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.638A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 311 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.618A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.601A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 156 through 158 removed outlier: 3.667A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.729A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS L 39 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.540A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA L 196 " --> pdb=" O ILE L 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 205 " --> pdb=" O ALA L 196 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1804 1.34 - 1.46: 1151 1.46 - 1.58: 3145 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 6165 Sorted by residual: bond pdb=" CA SER H 21 " pdb=" C SER H 21 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.19e-02 7.06e+03 5.21e+00 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" CA MET H 20 " pdb=" C MET H 20 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.20e-02 6.94e+03 3.66e+00 bond pdb=" CA LYS H 19 " pdb=" C LYS H 19 " ideal model delta sigma weight residual 1.521 1.543 -0.022 1.24e-02 6.50e+03 3.20e+00 bond pdb=" C SER L 208 " pdb=" O SER L 208 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.21e-02 6.83e+03 2.77e+00 ... (remaining 6160 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.12: 198 106.12 - 113.11: 3345 113.11 - 120.11: 2071 120.11 - 127.10: 2686 127.10 - 134.10: 86 Bond angle restraints: 8386 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.72 116.90 -6.18 1.01e+00 9.80e-01 3.74e+01 angle pdb=" N LYS L 207 " pdb=" CA LYS L 207 " pdb=" C LYS L 207 " ideal model delta sigma weight residual 108.76 99.12 9.64 1.69e+00 3.50e-01 3.25e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 115.29 -4.67 1.02e+00 9.61e-01 2.10e+01 angle pdb=" N ALA A 217 " pdb=" CA ALA A 217 " pdb=" C ALA A 217 " ideal model delta sigma weight residual 113.16 118.52 -5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" C PHE A 216 " ideal model delta sigma weight residual 111.36 116.02 -4.66 1.09e+00 8.42e-01 1.83e+01 ... (remaining 8381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3131 17.51 - 35.03: 403 35.03 - 52.54: 111 52.54 - 70.06: 13 70.06 - 87.57: 7 Dihedral angle restraints: 3665 sinusoidal: 1412 harmonic: 2253 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -6.91 -79.09 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS H 145 " pdb=" SG CYS H 145 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 38.53 54.47 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ALA H 92 " pdb=" C ALA H 92 " pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 805 0.059 - 0.118: 140 0.118 - 0.176: 12 0.176 - 0.235: 1 0.235 - 0.294: 1 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA LYS L 207 " pdb=" N LYS L 207 " pdb=" C LYS L 207 " pdb=" CB LYS L 207 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ALA A 217 " pdb=" N ALA A 217 " pdb=" C ALA A 217 " pdb=" CB ALA A 217 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 956 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 188 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO H 189 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO L 95 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 127 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO H 128 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 128 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 128 " 0.020 5.00e-02 4.00e+02 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 12 2.35 - 2.99: 3144 2.99 - 3.62: 8889 3.62 - 4.26: 13333 4.26 - 4.90: 23120 Nonbonded interactions: 48498 Sorted by model distance: nonbonded pdb=" O MET A 218 " pdb=" O THR A 219 " model vdw 1.709 3.040 nonbonded pdb=" CE MET H 20 " pdb=" CE MET H 81 " model vdw 1.734 3.880 nonbonded pdb=" N GLU L 187 " pdb=" OE1 GLU L 187 " model vdw 2.177 2.520 nonbonded pdb=" O GLY H 42 " pdb=" CG LYS H 43 " model vdw 2.212 3.440 nonbonded pdb=" OD1 ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.269 2.440 ... (remaining 48493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.950 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: 0.000 Extract box with map and model: 6.140 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.860 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.003 0.043 6165 Z= 0.195 Angle : 0.700 11.963 8386 Z= 0.377 Chirality : 0.045 0.294 959 Planarity : 0.004 0.040 1047 Dihedral : 16.539 87.569 2211 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.52 % Allowed : 31.57 % Favored : 64.90 % 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: 0.01 (0.31), residues: 772 helix: 1.63 (0.33), residues: 251 sheet: -0.23 (0.41), residues: 188 loop : -1.11 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 159 HIS 0.001 0.000 HIS L 198 PHE 0.007 0.001 PHE A 285 TYR 0.014 0.001 TYR L 173 ARG 0.004 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.743 Fit side-chains REVERT: L 207 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6888 (mmmm) outliers start: 24 outliers final: 21 residues processed: 170 average time/residue: 0.7191 time to fit residues: 131.3173 Evaluate side-chains 166 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 209 ASN A 262 ASN H 59 ASN H 196 GLN L 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6165 Z= 0.187 Angle : 0.610 9.457 8386 Z= 0.301 Chirality : 0.042 0.134 959 Planarity : 0.004 0.040 1047 Dihedral : 5.735 45.691 858 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.12 % Favored : 92.75 % Rotamer: Outliers : 4.55 % Allowed : 29.07 % Favored : 66.37 % 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: 0.01 (0.31), residues: 772 helix: 1.64 (0.32), residues: 260 sheet: -0.25 (0.40), residues: 206 loop : -1.21 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 96 HIS 0.001 0.000 HIS H 84 PHE 0.008 0.001 PHE A 37 TYR 0.009 0.001 TYR H 95 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.688 Fit side-chains REVERT: A 55 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 256 MET cc_start: 0.8397 (mmm) cc_final: 0.8145 (mmm) REVERT: L 79 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8131 (mp0) REVERT: L 207 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7604 (mmmm) outliers start: 31 outliers final: 14 residues processed: 162 average time/residue: 0.8020 time to fit residues: 139.6228 Evaluate side-chains 148 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 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 209 ASN A 262 ASN H 196 GLN L 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6165 Z= 0.205 Angle : 0.622 10.797 8386 Z= 0.301 Chirality : 0.042 0.136 959 Planarity : 0.004 0.040 1047 Dihedral : 4.823 38.379 839 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % Rotamer: Outliers : 4.85 % Allowed : 28.49 % Favored : 66.67 % 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: 0.02 (0.31), residues: 772 helix: 1.70 (0.32), residues: 259 sheet: -0.34 (0.39), residues: 206 loop : -1.18 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 163 HIS 0.001 0.000 HIS B 17 PHE 0.007 0.001 PHE H 102 TYR 0.011 0.001 TYR A 183 ARG 0.001 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 0.733 Fit side-chains REVERT: A 55 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 177 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8219 (tttp) REVERT: A 184 MET cc_start: 0.3806 (OUTLIER) cc_final: 0.3605 (ttt) REVERT: A 256 MET cc_start: 0.8469 (mmm) cc_final: 0.8116 (mmm) REVERT: L 77 ASN cc_start: 0.7819 (p0) cc_final: 0.7548 (m-40) REVERT: L 79 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8091 (mp0) REVERT: L 82 ASP cc_start: 0.9010 (m-30) cc_final: 0.8658 (m-30) REVERT: L 207 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7688 (mmmm) outliers start: 33 outliers final: 22 residues processed: 159 average time/residue: 0.7930 time to fit residues: 134.6650 Evaluate side-chains 148 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 0.0370 chunk 32 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN B 40 ASN L 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6165 Z= 0.146 Angle : 0.587 8.144 8386 Z= 0.285 Chirality : 0.041 0.129 959 Planarity : 0.004 0.041 1047 Dihedral : 4.601 38.315 837 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.01 % Rotamer: Outliers : 4.85 % Allowed : 28.34 % Favored : 66.81 % 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: 0.05 (0.31), residues: 772 helix: 1.73 (0.32), residues: 260 sheet: -0.36 (0.39), residues: 206 loop : -1.13 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 104 HIS 0.001 0.000 HIS B 17 PHE 0.006 0.001 PHE A 77 TYR 0.009 0.001 TYR A 146 ARG 0.001 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.735 Fit side-chains REVERT: A 55 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 184 MET cc_start: 0.3554 (OUTLIER) cc_final: 0.3345 (ttt) REVERT: A 219 THR cc_start: 0.7559 (m) cc_final: 0.7046 (p) REVERT: A 256 MET cc_start: 0.8501 (mmm) cc_final: 0.8100 (mmm) REVERT: L 77 ASN cc_start: 0.7767 (p0) cc_final: 0.7431 (m-40) REVERT: L 79 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8046 (mp0) REVERT: L 82 ASP cc_start: 0.8992 (m-30) cc_final: 0.8616 (m-30) REVERT: L 207 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7696 (mmmm) outliers start: 33 outliers final: 20 residues processed: 159 average time/residue: 0.7502 time to fit residues: 128.2665 Evaluate side-chains 152 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6165 Z= 0.168 Angle : 0.603 11.205 8386 Z= 0.292 Chirality : 0.042 0.166 959 Planarity : 0.004 0.040 1047 Dihedral : 4.651 38.498 837 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.85 % Allowed : 30.10 % Favored : 65.05 % 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: 0.05 (0.31), residues: 772 helix: 1.72 (0.32), residues: 259 sheet: -0.36 (0.39), residues: 206 loop : -1.11 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 104 HIS 0.001 0.000 HIS H 84 PHE 0.007 0.001 PHE L 98 TYR 0.012 0.001 TYR A 183 ARG 0.003 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.720 Fit side-chains REVERT: A 55 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 96 CYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 256 MET cc_start: 0.8577 (mmm) cc_final: 0.8153 (mmm) REVERT: L 53 ARG cc_start: 0.8458 (mmt-90) cc_final: 0.8252 (mmt-90) REVERT: L 77 ASN cc_start: 0.7751 (p0) cc_final: 0.7515 (m-40) REVERT: L 79 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8071 (mp0) REVERT: L 82 ASP cc_start: 0.8960 (m-30) cc_final: 0.8572 (m-30) REVERT: L 144 ILE cc_start: 0.8646 (pt) cc_final: 0.8445 (pt) REVERT: L 207 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7706 (mmmm) outliers start: 33 outliers final: 21 residues processed: 158 average time/residue: 0.7557 time to fit residues: 127.8920 Evaluate side-chains 154 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6165 Z= 0.182 Angle : 0.603 9.411 8386 Z= 0.293 Chirality : 0.042 0.144 959 Planarity : 0.004 0.040 1047 Dihedral : 4.702 38.723 837 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 5.58 % Allowed : 28.93 % Favored : 65.49 % 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: 0.06 (0.31), residues: 772 helix: 1.73 (0.32), residues: 259 sheet: -0.34 (0.38), residues: 206 loop : -1.12 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 159 HIS 0.001 0.000 HIS H 204 PHE 0.007 0.001 PHE A 285 TYR 0.008 0.001 TYR L 91 ARG 0.003 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.749 Fit side-chains REVERT: A 55 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 96 CYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8241 (m) REVERT: A 256 MET cc_start: 0.8522 (mmm) cc_final: 0.8069 (mmm) REVERT: L 77 ASN cc_start: 0.7737 (p0) cc_final: 0.7510 (m-40) REVERT: L 79 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8066 (mp0) REVERT: L 82 ASP cc_start: 0.8942 (m-30) cc_final: 0.8555 (m-30) REVERT: L 144 ILE cc_start: 0.8663 (pt) cc_final: 0.8455 (pt) REVERT: L 207 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7839 (mmmm) outliers start: 38 outliers final: 21 residues processed: 158 average time/residue: 0.7435 time to fit residues: 125.9726 Evaluate side-chains 155 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 61 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6165 Z= 0.197 Angle : 0.627 9.238 8386 Z= 0.303 Chirality : 0.042 0.136 959 Planarity : 0.004 0.040 1047 Dihedral : 4.741 38.681 837 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.85 % Allowed : 29.66 % Favored : 65.49 % 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: 0.05 (0.31), residues: 772 helix: 1.71 (0.32), residues: 259 sheet: -0.32 (0.39), residues: 201 loop : -1.14 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.007 0.001 PHE A 285 TYR 0.009 0.001 TYR L 91 ARG 0.003 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.732 Fit side-chains REVERT: A 55 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 96 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 221 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 256 MET cc_start: 0.8537 (mmm) cc_final: 0.8062 (mmm) REVERT: L 77 ASN cc_start: 0.7696 (p0) cc_final: 0.7482 (m-40) REVERT: L 79 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8085 (mp0) REVERT: L 82 ASP cc_start: 0.8948 (m-30) cc_final: 0.8584 (m-30) REVERT: L 144 ILE cc_start: 0.8680 (pt) cc_final: 0.8475 (pt) REVERT: L 207 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7835 (mmmm) outliers start: 33 outliers final: 22 residues processed: 156 average time/residue: 0.7379 time to fit residues: 123.4181 Evaluate side-chains 150 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 3 GLN H 40 ASN H 196 GLN L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6165 Z= 0.181 Angle : 0.611 8.220 8386 Z= 0.297 Chirality : 0.042 0.131 959 Planarity : 0.004 0.039 1047 Dihedral : 4.725 38.726 837 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.70 % Allowed : 30.25 % Favored : 65.05 % 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: 0.03 (0.31), residues: 772 helix: 1.73 (0.32), residues: 258 sheet: -0.33 (0.39), residues: 201 loop : -1.18 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.007 0.001 PHE L 98 TYR 0.009 0.001 TYR A 146 ARG 0.006 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.704 Fit side-chains REVERT: A 55 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8559 (mp) REVERT: A 96 CYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8267 (m) REVERT: A 256 MET cc_start: 0.8521 (mmm) cc_final: 0.8045 (mmm) REVERT: L 79 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8097 (mp0) REVERT: L 82 ASP cc_start: 0.8938 (m-30) cc_final: 0.8554 (m-30) REVERT: L 144 ILE cc_start: 0.8668 (pt) cc_final: 0.8437 (pt) REVERT: L 185 GLU cc_start: 0.7489 (pm20) cc_final: 0.7239 (pm20) REVERT: L 199 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7288 (mtmm) REVERT: L 207 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7753 (mmmm) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.7565 time to fit residues: 127.3131 Evaluate side-chains 159 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN H 3 GLN H 40 ASN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6165 Z= 0.278 Angle : 0.671 13.017 8386 Z= 0.326 Chirality : 0.044 0.149 959 Planarity : 0.004 0.038 1047 Dihedral : 4.982 38.428 837 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.99 % Allowed : 30.25 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 772 helix: 1.58 (0.32), residues: 259 sheet: -0.25 (0.40), residues: 195 loop : -1.25 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 159 HIS 0.002 0.001 HIS B 17 PHE 0.012 0.001 PHE H 102 TYR 0.011 0.001 TYR H 95 ARG 0.005 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.726 Fit side-chains REVERT: A 55 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 96 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 256 MET cc_start: 0.8608 (mmm) cc_final: 0.8112 (mmm) REVERT: L 53 ARG cc_start: 0.8512 (mmt-90) cc_final: 0.8236 (mmt-90) REVERT: L 79 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8087 (mp0) REVERT: L 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.8617 (m-30) outliers start: 34 outliers final: 22 residues processed: 154 average time/residue: 0.8405 time to fit residues: 137.9145 Evaluate side-chains 151 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 106 ASN A 209 ASN L 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6165 Z= 0.208 Angle : 0.647 9.532 8386 Z= 0.315 Chirality : 0.043 0.137 959 Planarity : 0.004 0.038 1047 Dihedral : 4.936 38.293 837 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.67 % Allowed : 32.16 % Favored : 64.17 % 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: -0.11 (0.31), residues: 772 helix: 1.56 (0.32), residues: 259 sheet: -0.37 (0.39), residues: 200 loop : -1.24 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.007 0.001 PHE A 77 TYR 0.009 0.001 TYR A 146 ARG 0.005 0.000 ARG L 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.742 Fit side-chains REVERT: A 55 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 96 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8294 (m) REVERT: A 256 MET cc_start: 0.8582 (mmm) cc_final: 0.8081 (mmm) REVERT: L 79 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8105 (mp0) REVERT: L 82 ASP cc_start: 0.8967 (m-30) cc_final: 0.8606 (m-30) outliers start: 25 outliers final: 21 residues processed: 152 average time/residue: 0.7979 time to fit residues: 129.6320 Evaluate side-chains 148 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain L residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 106 ASN A 209 ASN H 40 ASN L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100232 restraints weight = 9016.020| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.68 r_work: 0.3055 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6165 Z= 0.172 Angle : 0.633 9.580 8386 Z= 0.308 Chirality : 0.042 0.131 959 Planarity : 0.004 0.038 1047 Dihedral : 4.777 37.488 837 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.67 % Allowed : 32.45 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 772 helix: 1.64 (0.32), residues: 259 sheet: -0.35 (0.39), residues: 200 loop : -1.21 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.006 0.001 PHE A 244 TYR 0.010 0.001 TYR A 183 ARG 0.005 0.000 ARG L 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2881.00 seconds wall clock time: 51 minutes 54.61 seconds (3114.61 seconds total)