Starting phenix.real_space_refine on Fri Dec 8 07:05:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/12_2023/8hr5_34958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/12_2023/8hr5_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_34958/12_2023/8hr5_34958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/12_2023/8hr5_34958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/12_2023/8hr5_34958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr5_34958/12_2023/8hr5_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.13, per 1000 atoms: 0.68 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: 3.95 Conformation dependent library (CDL) restraints added in 1.1 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: 2.56 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: 2.72 Time building geometry restraints manager: 4.16 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: 4318 35.63 - 71.25: 348 71.25 - 106.88: 27 106.88 - 142.51: 2 142.51 - 178.13: 5 Dihedral angle restraints: 4700 sinusoidal: 2604 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 4697 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.820 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.710 Find NCS groups from input model: 0.170 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- 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 : 22.195 178.134 3336 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 : 0.621 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 102 average time/residue: 0.2175 time to fit residues: 29.0668 Evaluate side-chains 70 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0644 time to fit residues: 0.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7964 Z= 0.264 Angle : 0.625 9.252 11398 Z= 0.325 Chirality : 0.036 0.180 1434 Planarity : 0.004 0.040 1009 Dihedral : 23.020 174.270 2431 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 2.64 % Allowed : 14.18 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.32), residues: 699 helix: 2.34 (0.27), residues: 357 sheet: -0.88 (0.51), residues: 103 loop : -1.12 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.007 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 91 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.610 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.1489 time to fit residues: 18.5724 Evaluate side-chains 76 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.0705 time to fit residues: 1.9041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.0060 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7964 Z= 0.167 Angle : 0.530 8.463 11398 Z= 0.278 Chirality : 0.034 0.216 1434 Planarity : 0.003 0.035 1009 Dihedral : 22.710 175.827 2431 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % 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: 1.81 (0.33), residues: 699 helix: 3.15 (0.27), residues: 358 sheet: -0.68 (0.53), residues: 97 loop : -1.07 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS A 160 PHE 0.011 0.001 PHE A 370 TYR 0.017 0.001 TYR A 417 ARG 0.009 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 87 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.648 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.1608 time to fit residues: 19.4670 Evaluate side-chains 73 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0750 time to fit residues: 1.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 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: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7964 Z= 0.398 Angle : 0.704 7.881 11398 Z= 0.366 Chirality : 0.039 0.187 1434 Planarity : 0.004 0.036 1009 Dihedral : 22.905 176.965 2431 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.05 % Allowed : 19.95 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.33), residues: 699 helix: 2.59 (0.27), residues: 361 sheet: -1.11 (0.49), residues: 110 loop : -1.39 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 24 HIS 0.007 0.002 HIS A 160 PHE 0.024 0.003 PHE A 370 TYR 0.023 0.003 TYR A 150 ARG 0.003 0.000 ARG B 202 *********************** 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 90 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.713 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 82 average time/residue: 0.1410 time to fit residues: 17.3578 Evaluate side-chains 78 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.0733 time to fit residues: 2.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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: 0.7080 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7964 Z= 0.180 Angle : 0.536 6.697 11398 Z= 0.283 Chirality : 0.034 0.217 1434 Planarity : 0.003 0.036 1009 Dihedral : 22.696 177.529 2431 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.92 % Allowed : 22.12 % Favored : 75.96 % 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: 1.69 (0.33), residues: 699 helix: 3.17 (0.27), residues: 360 sheet: -1.17 (0.51), residues: 102 loop : -1.16 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.002 PHE A 319 TYR 0.016 0.001 TYR A 417 ARG 0.002 0.000 ARG B 134 *********************** 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 84 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.695 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 0.1518 time to fit residues: 18.4680 Evaluate side-chains 70 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0749 time to fit residues: 1.4478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.3053 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= 0.213 Angle : 0.554 6.885 11398 Z= 0.291 Chirality : 0.035 0.183 1434 Planarity : 0.003 0.034 1009 Dihedral : 22.627 178.572 2431 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.12 % Allowed : 24.28 % Favored : 72.60 % 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: 1.72 (0.33), residues: 699 helix: 3.26 (0.27), residues: 359 sheet: -1.26 (0.51), residues: 102 loop : -1.19 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.004 0.001 HIS A 160 PHE 0.018 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 80 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.677 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.1452 time to fit residues: 16.4367 Evaluate side-chains 73 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1016 time to fit residues: 2.5448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7964 Z= 0.173 Angle : 0.521 6.332 11398 Z= 0.275 Chirality : 0.034 0.184 1434 Planarity : 0.003 0.034 1009 Dihedral : 22.567 178.648 2431 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.64 % Allowed : 23.80 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 699 helix: 3.43 (0.26), residues: 359 sheet: -1.20 (0.49), residues: 108 loop : -1.29 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.019 0.002 PHE A 319 TYR 0.016 0.001 TYR A 417 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 82 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.824 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 0.1302 time to fit residues: 16.3010 Evaluate side-chains 68 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0741 time to fit residues: 1.6689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7124 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7964 Z= 0.234 Angle : 0.562 6.730 11398 Z= 0.296 Chirality : 0.035 0.180 1434 Planarity : 0.003 0.034 1009 Dihedral : 22.594 178.933 2431 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.16 % Allowed : 26.68 % Favored : 71.15 % 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: 1.72 (0.33), residues: 699 helix: 3.30 (0.26), residues: 359 sheet: -0.97 (0.49), residues: 117 loop : -1.43 (0.39), residues: 223 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 0.015 0.002 PHE A 370 TYR 0.017 0.002 TYR A 150 ARG 0.002 0.000 ARG B 134 *********************** 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 74 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.615 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.1343 time to fit residues: 14.5476 Evaluate side-chains 71 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0744 time to fit residues: 1.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.0060 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.7048 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7964 Z= 0.158 Angle : 0.513 6.734 11398 Z= 0.272 Chirality : 0.034 0.195 1434 Planarity : 0.003 0.033 1009 Dihedral : 22.524 178.462 2431 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.48 % Allowed : 26.68 % Favored : 72.84 % 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: 1.90 (0.33), residues: 699 helix: 3.47 (0.26), residues: 360 sheet: -0.89 (0.48), residues: 117 loop : -1.40 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 24 HIS 0.002 0.001 HIS A 160 PHE 0.017 0.001 PHE A 319 TYR 0.019 0.001 TYR A 417 ARG 0.002 0.000 ARG A 330 *********************** 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 71 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.661 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1346 time to fit residues: 14.6410 Evaluate side-chains 64 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0739 time to fit residues: 0.9762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.7217 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7964 Z= 0.397 Angle : 0.697 7.669 11398 Z= 0.363 Chirality : 0.039 0.177 1434 Planarity : 0.004 0.035 1009 Dihedral : 22.745 179.209 2431 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.20 % Allowed : 27.16 % Favored : 71.63 % 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: 1.28 (0.33), residues: 699 helix: 2.81 (0.26), residues: 362 sheet: -0.98 (0.50), residues: 114 loop : -1.55 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 24 HIS 0.006 0.001 HIS A 160 PHE 0.023 0.003 PHE A 370 TYR 0.025 0.003 TYR A 150 ARG 0.003 0.001 ARG A 5 ********************** 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 69 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.680 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.1405 time to fit residues: 14.8310 Evaluate side-chains 68 residues out of total 661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0694 time to fit residues: 1.4118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.175293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142084 restraints weight = 11858.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141521 restraints weight = 16568.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142757 restraints weight = 13535.294| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3629 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= 0.188 Angle : 0.552 7.549 11398 Z= 0.293 Chirality : 0.035 0.196 1434 Planarity : 0.003 0.036 1009 Dihedral : 22.617 178.440 2431 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.48 % Allowed : 27.88 % Favored : 71.63 % 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: 3.26 (0.27), residues: 362 sheet: -0.86 (0.50), residues: 114 loop : -1.58 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.001 PHE A 370 TYR 0.021 0.002 TYR A 417 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: 1410.55 seconds wall clock time: 26 minutes 24.83 seconds (1584.83 seconds total)