Starting phenix.real_space_refine on Fri Apr 5 20:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/04_2024/8p77_17520_updated.pdb" } resolution = 1.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 31 5.16 5 C 3313 2.51 5 N 876 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 247": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5271 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 58 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 29 Unusual residues: {'I73': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 29 Unusual residues: {'I73': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C11AI73 J 401 " occ=0.50 ... (56 atoms not shown) pdb=" O1 BI73 J 401 " occ=0.50 Time building chain proxies: 3.60, per 1000 atoms: 0.68 Number of scatterers: 5271 At special positions: 0 Unit cell: (84.7875, 93.3375, 67.6875, 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 31 16.00 O 1051 8.00 N 876 7.00 C 3313 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: 2.13 Conformation dependent library (CDL) restraints added in 934.7 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 2 sheets defined 53.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'H' and resid 266 through 269 No H-bonds generated for 'chain 'H' and resid 266 through 269' Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.669A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.687A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.805A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.901A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 224 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 242 through 261 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 192 through 208 removed outlier: 4.543A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 83 removed outlier: 6.692A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 216 hydrogen bonds defined for protein. 567 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: 1.36 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1170 1.46 - 1.58: 2398 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5261 Sorted by residual: bond pdb=" C3 AI73 J 401 " pdb=" N10AI73 J 401 " ideal model delta sigma weight residual 1.339 1.517 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C3 BI73 J 401 " pdb=" N10BI73 J 401 " ideal model delta sigma weight residual 1.339 1.516 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C5 BI73 J 401 " pdb=" N18BI73 J 401 " ideal model delta sigma weight residual 1.349 1.480 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C5 AI73 J 401 " pdb=" N18AI73 J 401 " ideal model delta sigma weight residual 1.349 1.480 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" N1 AI73 J 401 " pdb=" N2 AI73 J 401 " ideal model delta sigma weight residual 1.343 1.415 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 5256 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.22: 171 106.22 - 113.15: 2805 113.15 - 120.07: 1854 120.07 - 127.00: 2219 127.00 - 133.93: 72 Bond angle restraints: 7121 Sorted by residual: angle pdb=" C4 BI73 J 401 " pdb=" C3 BI73 J 401 " pdb=" N10BI73 J 401 " ideal model delta sigma weight residual 127.16 119.93 7.23 3.00e+00 1.11e-01 5.81e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.65 4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" C4 AI73 J 401 " pdb=" C3 AI73 J 401 " pdb=" N10AI73 J 401 " ideal model delta sigma weight residual 127.16 120.17 6.99 3.00e+00 1.11e-01 5.44e+00 angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.39 -6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" C8 BI73 J 401 " pdb=" C9 BI73 J 401 " pdb=" N1 BI73 J 401 " ideal model delta sigma weight residual 113.59 107.37 6.22 3.00e+00 1.11e-01 4.30e+00 ... (remaining 7116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.84: 2806 18.84 - 37.68: 287 37.68 - 56.51: 63 56.51 - 75.35: 19 75.35 - 94.19: 6 Dihedral angle restraints: 3181 sinusoidal: 1334 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" C41AI73 J 401 " pdb=" C40AI73 J 401 " pdb=" N18AI73 J 401 " pdb=" C5 AI73 J 401 " ideal model delta sinusoidal sigma weight residual 166.20 -99.61 -94.19 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB GLU J 99 " pdb=" CG GLU J 99 " pdb=" CD GLU J 99 " pdb=" OE1 GLU J 99 " ideal model delta sinusoidal sigma weight residual 0.00 -88.27 88.27 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 495 0.028 - 0.057: 170 0.057 - 0.085: 72 0.085 - 0.114: 36 0.114 - 0.142: 6 Chirality restraints: 779 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 776 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO J 140 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.60e+00 pdb=" C ASP I 193 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 199 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL J 199 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL J 199 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY J 200 " 0.007 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 992 2.76 - 3.30: 5310 3.30 - 3.83: 10074 3.83 - 4.37: 11868 4.37 - 4.90: 19336 Nonbonded interactions: 47580 Sorted by model distance: nonbonded pdb=" OD2 ASP J 97 " pdb=" O HOH J 501 " model vdw 2.228 2.440 nonbonded pdb=" O HOH J 514 " pdb=" O HOH J 552 " model vdw 2.255 2.440 nonbonded pdb=" O PHE J 295 " pdb=" O HOH J 502 " model vdw 2.263 2.440 nonbonded pdb=" O HOH I 403 " pdb=" O HOH I 445 " model vdw 2.265 2.440 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.277 2.440 ... (remaining 47575 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=0.50 max=1.00 mean=0.99 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: 3.140 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: 14.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.580 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 0.178 5261 Z= 0.436 Angle : 0.583 7.229 7121 Z= 0.275 Chirality : 0.039 0.142 779 Planarity : 0.004 0.035 905 Dihedral : 16.680 94.189 1985 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 14.98 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.34), residues: 618 helix: 2.07 (0.29), residues: 339 sheet: 1.40 (1.58), residues: 10 loop : 0.48 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 60 ARG 0.007 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.615 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 106 average time/residue: 1.4520 time to fit residues: 159.6952 Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5261 Z= 0.168 Angle : 0.500 5.789 7121 Z= 0.254 Chirality : 0.039 0.137 779 Planarity : 0.004 0.033 905 Dihedral : 8.233 93.167 730 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 14.26 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.34), residues: 618 helix: 2.03 (0.29), residues: 339 sheet: 1.51 (1.63), residues: 10 loop : 0.45 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.003 0.001 HIS I 281 PHE 0.013 0.002 PHE J 91 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.595 Fit side-chains REVERT: J 92 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7121 (m-30) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 1.4701 time to fit residues: 163.1066 Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5261 Z= 0.234 Angle : 0.563 6.202 7121 Z= 0.288 Chirality : 0.041 0.143 779 Planarity : 0.005 0.034 905 Dihedral : 7.988 91.644 724 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 13.18 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 618 helix: 1.76 (0.28), residues: 340 sheet: 1.18 (1.55), residues: 10 loop : 0.42 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.006 0.001 HIS I 281 PHE 0.015 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.004 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.680 Fit side-chains REVERT: J 92 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7209 (m-30) outliers start: 13 outliers final: 6 residues processed: 112 average time/residue: 1.4406 time to fit residues: 167.6692 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5261 Z= 0.223 Angle : 0.552 6.085 7121 Z= 0.283 Chirality : 0.041 0.144 779 Planarity : 0.005 0.035 905 Dihedral : 7.960 91.440 724 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.07 % Allowed : 13.00 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.34), residues: 618 helix: 1.70 (0.28), residues: 340 sheet: 1.05 (1.48), residues: 10 loop : 0.41 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.015 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.004 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.635 Fit side-chains REVERT: J 42 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5286 (mmmt) REVERT: J 92 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7209 (m-30) outliers start: 17 outliers final: 7 residues processed: 113 average time/residue: 1.4515 time to fit residues: 170.0329 Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5261 Z= 0.218 Angle : 0.550 6.081 7121 Z= 0.282 Chirality : 0.041 0.144 779 Planarity : 0.005 0.035 905 Dihedral : 7.929 91.308 724 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 13.18 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.34), residues: 618 helix: 1.71 (0.28), residues: 340 sheet: 1.26 (1.56), residues: 10 loop : 0.39 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.015 0.002 PHE J 295 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.614 Fit side-chains REVERT: J 42 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5164 (mmmt) REVERT: J 92 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: J 216 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6815 (p0) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 1.4661 time to fit residues: 165.5925 Evaluate side-chains 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5261 Z= 0.159 Angle : 0.494 5.749 7121 Z= 0.252 Chirality : 0.039 0.139 779 Planarity : 0.005 0.034 905 Dihedral : 7.709 91.624 724 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 14.62 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.34), residues: 618 helix: 1.98 (0.28), residues: 339 sheet: 1.72 (1.68), residues: 10 loop : 0.48 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.012 0.002 PHE I 110 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.664 Fit side-chains REVERT: I 141 GLU cc_start: 0.7192 (tp30) cc_final: 0.6958 (tp30) REVERT: J 42 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5125 (mmmt) REVERT: J 92 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7161 (m-30) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 1.4511 time to fit residues: 159.6355 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5261 Z= 0.273 Angle : 0.597 6.362 7121 Z= 0.306 Chirality : 0.043 0.145 779 Planarity : 0.005 0.036 905 Dihedral : 7.908 90.240 723 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 14.62 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.33), residues: 618 helix: 1.58 (0.28), residues: 342 sheet: 1.18 (1.55), residues: 10 loop : 0.42 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.007 0.002 HIS I 281 PHE 0.018 0.003 PHE J 81 TYR 0.023 0.002 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.618 Fit side-chains REVERT: J 42 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5170 (mmmt) REVERT: J 92 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: J 216 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6765 (p0) outliers start: 11 outliers final: 5 residues processed: 111 average time/residue: 1.4104 time to fit residues: 162.7536 Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5261 Z= 0.183 Angle : 0.526 5.884 7121 Z= 0.268 Chirality : 0.040 0.141 779 Planarity : 0.005 0.034 905 Dihedral : 7.743 91.018 723 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 15.34 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 618 helix: 1.82 (0.28), residues: 339 sheet: 1.62 (1.66), residues: 10 loop : 0.44 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.003 0.001 HIS I 281 PHE 0.014 0.002 PHE J 295 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.603 Fit side-chains REVERT: I 141 GLU cc_start: 0.7256 (tp30) cc_final: 0.6969 (tp30) REVERT: J 42 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5104 (mmmt) REVERT: J 92 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7187 (m-30) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 1.3875 time to fit residues: 155.6165 Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5261 Z= 0.203 Angle : 0.545 6.050 7121 Z= 0.279 Chirality : 0.041 0.142 779 Planarity : 0.005 0.037 905 Dihedral : 7.752 91.339 723 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 15.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 618 helix: 1.76 (0.28), residues: 340 sheet: 1.60 (1.67), residues: 10 loop : 0.45 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.014 0.002 PHE J 295 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.754 Fit side-chains REVERT: I 141 GLU cc_start: 0.7260 (tp30) cc_final: 0.6967 (tp30) REVERT: J 42 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.5131 (mmmt) REVERT: J 92 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: J 216 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6816 (p0) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 1.4515 time to fit residues: 162.8567 Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5261 Z= 0.195 Angle : 0.540 7.240 7121 Z= 0.275 Chirality : 0.040 0.142 779 Planarity : 0.005 0.037 905 Dihedral : 7.738 91.323 723 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 15.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 618 helix: 1.81 (0.28), residues: 339 sheet: 1.69 (1.68), residues: 10 loop : 0.45 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.014 0.002 PHE J 295 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.001 ARG H 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.599 Fit side-chains REVERT: I 141 GLU cc_start: 0.7244 (tp30) cc_final: 0.6951 (tp30) REVERT: J 42 LYS cc_start: 0.5724 (OUTLIER) cc_final: 0.5109 (mmmt) REVERT: J 92 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: J 216 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6808 (p0) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 1.4098 time to fit residues: 157.9337 Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.171518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144492 restraints weight = 17355.272| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.00 r_work: 0.3674 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5261 Z= 0.211 Angle : 0.558 7.178 7121 Z= 0.285 Chirality : 0.041 0.142 779 Planarity : 0.005 0.038 905 Dihedral : 7.770 91.320 723 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.34), residues: 618 helix: 1.72 (0.28), residues: 340 sheet: 1.57 (1.66), residues: 10 loop : 0.45 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.018 0.002 PHE J 81 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 ARG H 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.61 seconds wall clock time: 58 minutes 39.46 seconds (3519.46 seconds total)