Starting phenix.real_space_refine on Tue Feb 13 20:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/02_2024/8hr5_34958.pdb" } resolution = 3.73 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 17 5.16 5 C 4339 2.51 5 N 1351 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 222": "OE1" <-> "OE2" 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: 7595 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3327 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'GLU:plan': 25, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1660 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 3, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 50, 'rna3p_pyr': 41} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 3 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Time building chain proxies: 5.25, per 1000 atoms: 0.69 Number of scatterers: 7595 At special positions: 0 Unit cell: (80.36, 117.26, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 123 15.00 O 1765 8.00 N 1351 7.00 C 4339 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: 3.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 55.3% alpha, 12.2% beta 42 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 53 removed outlier: 3.616A pdb=" N ARG A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.974A pdb=" N GLU A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 131 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.218A pdb=" N LEU A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.672A pdb=" N ASP A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.620A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 340 removed outlier: 3.517A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.045A pdb=" N LYS A 344 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 345 through 382 removed outlier: 3.618A pdb=" N ASN A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.646A pdb=" N LEU A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'B' and resid 14 through 52 removed outlier: 3.546A pdb=" N TYR B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.944A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 148 removed outlier: 4.314A pdb=" N VAL B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 4.384A pdb=" N SER B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.792A pdb=" N LEU B 206 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.855A pdb=" N HIS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 267 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 216 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 207 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 253 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 302 removed outlier: 5.400A pdb=" N VAL A 289 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 390 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 291 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.521A pdb=" N THR B 201 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 257 " --> pdb=" O THR B 201 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1314 1.33 - 1.45: 2528 1.45 - 1.57: 3856 1.57 - 1.69: 239 1.69 - 1.81: 27 Bond restraints: 7964 Sorted by residual: bond pdb=" O3' A C 79 " pdb=" P U C 80 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.63e+01 bond pdb=" O3' G C 99 " pdb=" P A C 100 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" N VAL A 4 " pdb=" CA VAL A 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.08e+00 bond pdb=" N ILE A 120 " pdb=" CA ILE A 120 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.82e+00 ... (remaining 7959 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.32: 735 106.32 - 113.24: 4541 113.24 - 120.16: 2854 120.16 - 127.08: 2967 127.08 - 134.01: 301 Bond angle restraints: 11398 Sorted by residual: angle pdb=" N GLY A 55 " pdb=" CA GLY A 55 " pdb=" C GLY A 55 " ideal model delta sigma weight residual 113.24 107.38 5.86 1.31e+00 5.83e-01 2.00e+01 angle pdb=" N MET A 221 " pdb=" CA MET A 221 " pdb=" C MET A 221 " ideal model delta sigma weight residual 110.80 118.65 -7.85 2.13e+00 2.20e-01 1.36e+01 angle pdb=" C3' G C 91 " pdb=" O3' G C 91 " pdb=" P U C 92 " ideal model delta sigma weight residual 120.20 125.26 -5.06 1.50e+00 4.44e-01 1.14e+01 angle pdb=" N GLU A 222 " pdb=" CA GLU A 222 " pdb=" C GLU A 222 " ideal model delta sigma weight residual 111.39 115.89 -4.50 1.38e+00 5.25e-01 1.06e+01 angle pdb=" CA THR A 10 " pdb=" C THR A 10 " pdb=" O THR A 10 " ideal model delta sigma weight residual 121.33 117.96 3.37 1.08e+00 8.57e-01 9.72e+00 ... (remaining 11393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 4377 35.63 - 71.25: 405 71.25 - 106.88: 27 106.88 - 142.51: 2 142.51 - 178.13: 5 Dihedral angle restraints: 4816 sinusoidal: 2720 harmonic: 2096 Sorted by residual: dihedral pdb=" O4' U C 94 " pdb=" C1' U C 94 " pdb=" N1 U C 94 " pdb=" C2 U C 94 " ideal model delta sinusoidal sigma weight residual 200.00 29.81 170.19 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U C 77 " pdb=" C1' U C 77 " pdb=" N1 U C 77 " pdb=" C2 U C 77 " ideal model delta sinusoidal sigma weight residual 200.00 41.62 158.38 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U C 76 " pdb=" C1' U C 76 " pdb=" N1 U C 76 " pdb=" C2 U C 76 " ideal model delta sinusoidal sigma weight residual 232.00 61.11 170.89 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 4813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1153 0.048 - 0.097: 186 0.097 - 0.145: 49 0.145 - 0.193: 41 0.193 - 0.241: 5 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA MET A 221 " pdb=" N MET A 221 " pdb=" C MET A 221 " pdb=" CB MET A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' G C 91 " pdb=" C4' G C 91 " pdb=" O3' G C 91 " pdb=" C2' G C 91 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A C 207 " pdb=" C4' A C 207 " pdb=" O3' A C 207 " pdb=" C2' A C 207 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1431 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 27 " -0.027 2.00e-02 2.50e+03 1.21e-02 4.41e+00 pdb=" N9 G C 27 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G C 27 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 27 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G C 27 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 27 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 40 " 0.022 2.00e-02 2.50e+03 1.18e-02 3.13e+00 pdb=" N1 C C 40 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 40 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C C 40 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 40 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 40 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C C 40 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C C 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 90 " -0.011 2.00e-02 2.50e+03 1.06e-02 2.52e+00 pdb=" N1 U C 90 " -0.003 2.00e-02 2.50e+03 pdb=" C2 U C 90 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U C 90 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U C 90 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U C 90 " -0.011 2.00e-02 2.50e+03 pdb=" C6 U C 90 " 0.023 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 7314 3.27 - 3.82: 13145 3.82 - 4.36: 14335 4.36 - 4.90: 22495 Nonbonded interactions: 57976 Sorted by model distance: nonbonded pdb=" O2' G C 74 " pdb=" O4' G C 75 " model vdw 2.191 2.440 nonbonded pdb=" O2' A C 71 " pdb=" O4' A C 72 " model vdw 2.195 2.440 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.244 2.440 nonbonded pdb=" O2 U C 87 " pdb=" O6 G C 99 " model vdw 2.246 2.432 nonbonded pdb=" O4 U C 47 " pdb=" O6 G C 68 " model vdw 2.246 2.432 ... (remaining 57971 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.970 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.900 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7964 Z= 0.282 Angle : 0.673 7.848 11398 Z= 0.420 Chirality : 0.048 0.241 1434 Planarity : 0.003 0.040 1009 Dihedral : 22.930 178.134 3452 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.37 % Allowed : 2.16 % Favored : 94.47 % 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: 0.07 (0.32), residues: 699 helix: 1.21 (0.27), residues: 352 sheet: -1.12 (0.55), residues: 90 loop : -1.10 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.013 0.002 PHE A 370 TYR 0.018 0.002 TYR A 150 ARG 0.002 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.701 Fit side-chains REVERT: B 52 ASN cc_start: 0.8797 (t0) cc_final: 0.8536 (t0) REVERT: B 63 ASP cc_start: 0.5379 (t0) cc_final: 0.5051 (t0) REVERT: B 147 ASP cc_start: 0.8139 (t70) cc_final: 0.7926 (t0) outliers start: 14 outliers final: 1 residues processed: 102 average time/residue: 0.2225 time to fit residues: 29.7506 Evaluate side-chains 71 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7964 Z= 0.262 Angle : 0.624 9.250 11398 Z= 0.325 Chirality : 0.036 0.183 1434 Planarity : 0.004 0.041 1009 Dihedral : 23.772 174.330 2548 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 2.40 % Allowed : 14.66 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.32), residues: 699 helix: 2.38 (0.27), residues: 356 sheet: -0.90 (0.51), residues: 103 loop : -1.23 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 PHE 0.019 0.002 PHE A 370 TYR 0.023 0.002 TYR A 150 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.667 Fit side-chains REVERT: B 8 LYS cc_start: 0.6938 (tmtt) cc_final: 0.6569 (ttpt) REVERT: B 63 ASP cc_start: 0.5577 (t0) cc_final: 0.5278 (t0) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.1372 time to fit residues: 16.8767 Evaluate side-chains 75 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7964 Z= 0.219 Angle : 0.569 7.988 11398 Z= 0.298 Chirality : 0.035 0.212 1434 Planarity : 0.003 0.036 1009 Dihedral : 23.462 175.667 2547 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.37 % Allowed : 17.79 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 699 helix: 2.95 (0.27), residues: 359 sheet: -0.94 (0.50), residues: 108 loop : -1.20 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 220 HIS 0.005 0.001 HIS A 160 PHE 0.015 0.002 PHE A 370 TYR 0.017 0.002 TYR A 417 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.648 Fit side-chains REVERT: B 63 ASP cc_start: 0.5624 (t0) cc_final: 0.5355 (t0) REVERT: B 192 ASN cc_start: 0.7760 (t0) cc_final: 0.7533 (t0) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.1625 time to fit residues: 19.1497 Evaluate side-chains 75 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7964 Z= 0.270 Angle : 0.602 7.282 11398 Z= 0.316 Chirality : 0.036 0.203 1434 Planarity : 0.003 0.038 1009 Dihedral : 23.470 176.274 2547 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 4.57 % Allowed : 21.15 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.33), residues: 699 helix: 2.96 (0.27), residues: 359 sheet: -1.15 (0.50), residues: 108 loop : -1.34 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 PHE 0.018 0.002 PHE A 370 TYR 0.021 0.002 TYR A 150 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.671 Fit side-chains REVERT: A 178 ASP cc_start: 0.7038 (t70) cc_final: 0.6818 (t0) REVERT: B 63 ASP cc_start: 0.5780 (t0) cc_final: 0.5561 (t0) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1434 time to fit residues: 17.1921 Evaluate side-chains 80 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.0010 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7964 Z= 0.291 Angle : 0.615 7.525 11398 Z= 0.325 Chirality : 0.037 0.184 1434 Planarity : 0.003 0.038 1009 Dihedral : 23.497 177.690 2547 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.49 % Allowed : 20.19 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.33), residues: 699 helix: 2.92 (0.27), residues: 359 sheet: -1.08 (0.51), residues: 110 loop : -1.37 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.004 0.001 HIS A 160 PHE 0.019 0.002 PHE A 370 TYR 0.021 0.002 TYR A 150 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.706 Fit side-chains REVERT: B 8 LYS cc_start: 0.7012 (ttpt) cc_final: 0.6603 (ttpt) outliers start: 27 outliers final: 19 residues processed: 88 average time/residue: 0.1311 time to fit residues: 17.8370 Evaluate side-chains 81 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 257 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7964 Z= 0.191 Angle : 0.541 6.534 11398 Z= 0.288 Chirality : 0.034 0.174 1434 Planarity : 0.003 0.036 1009 Dihedral : 23.351 177.936 2547 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.05 % Allowed : 23.56 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.33), residues: 699 helix: 3.23 (0.27), residues: 358 sheet: -1.28 (0.50), residues: 108 loop : -1.41 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.020 0.002 PHE A 319 TYR 0.015 0.002 TYR A 417 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.691 Fit side-chains REVERT: B 8 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6574 (ttpt) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.1347 time to fit residues: 16.8004 Evaluate side-chains 81 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7964 Z= 0.191 Angle : 0.536 6.493 11398 Z= 0.285 Chirality : 0.034 0.177 1434 Planarity : 0.003 0.035 1009 Dihedral : 23.303 178.154 2547 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.49 % Allowed : 22.60 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.33), residues: 699 helix: 3.30 (0.27), residues: 361 sheet: -1.25 (0.50), residues: 109 loop : -1.39 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.011 0.001 PHE A 370 TYR 0.016 0.002 TYR A 367 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.657 Fit side-chains REVERT: B 8 LYS cc_start: 0.7005 (ttpt) cc_final: 0.6515 (ttpt) outliers start: 27 outliers final: 22 residues processed: 87 average time/residue: 0.1308 time to fit residues: 17.6572 Evaluate side-chains 87 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 52 ASN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 7964 Z= 0.544 Angle : 0.819 8.596 11398 Z= 0.425 Chirality : 0.044 0.218 1434 Planarity : 0.005 0.040 1009 Dihedral : 23.705 179.610 2547 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.72 % Favored : 93.13 % Rotamer: Outliers : 7.93 % Allowed : 22.36 % Favored : 69.71 % 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: 0.74 (0.33), residues: 699 helix: 2.31 (0.26), residues: 362 sheet: -1.38 (0.51), residues: 109 loop : -1.58 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 24 HIS 0.008 0.002 HIS A 160 PHE 0.033 0.004 PHE A 370 TYR 0.027 0.003 TYR A 150 ARG 0.005 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 63 time to evaluate : 0.686 Fit side-chains REVERT: B 8 LYS cc_start: 0.7000 (ttpt) cc_final: 0.6549 (ttpt) outliers start: 33 outliers final: 29 residues processed: 87 average time/residue: 0.1296 time to fit residues: 17.4457 Evaluate side-chains 91 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 257 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7964 Z= 0.191 Angle : 0.563 6.764 11398 Z= 0.301 Chirality : 0.035 0.179 1434 Planarity : 0.003 0.039 1009 Dihedral : 23.415 179.247 2547 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.01 % Allowed : 24.76 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.33), residues: 699 helix: 3.08 (0.27), residues: 359 sheet: -0.91 (0.54), residues: 101 loop : -1.58 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.001 PHE A 370 TYR 0.018 0.002 TYR A 367 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.685 Fit side-chains REVERT: A 275 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8545 (mt) outliers start: 25 outliers final: 16 residues processed: 82 average time/residue: 0.1239 time to fit residues: 15.9114 Evaluate side-chains 75 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7964 Z= 0.313 Angle : 0.639 7.714 11398 Z= 0.335 Chirality : 0.038 0.182 1434 Planarity : 0.004 0.038 1009 Dihedral : 23.483 179.717 2547 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.53 % Allowed : 25.72 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.33), residues: 699 helix: 2.88 (0.27), residues: 360 sheet: -1.17 (0.52), residues: 106 loop : -1.57 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 PHE 0.020 0.002 PHE A 370 TYR 0.019 0.002 TYR A 252 ARG 0.002 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.718 Fit side-chains REVERT: A 275 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8621 (mt) outliers start: 23 outliers final: 21 residues processed: 79 average time/residue: 0.1309 time to fit residues: 16.0171 Evaluate side-chains 84 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138306 restraints weight = 11879.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139969 restraints weight = 11485.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140571 restraints weight = 9910.410| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7964 Z= 0.194 Angle : 0.556 7.716 11398 Z= 0.296 Chirality : 0.035 0.184 1434 Planarity : 0.003 0.038 1009 Dihedral : 23.398 179.265 2547 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.01 % Allowed : 25.48 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.34), residues: 699 helix: 3.16 (0.27), residues: 362 sheet: -1.04 (0.52), residues: 107 loop : -1.53 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.001 PHE A 370 TYR 0.018 0.002 TYR A 367 ARG 0.002 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.50 seconds wall clock time: 27 minutes 30.34 seconds (1650.34 seconds total)