Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:00:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0j_22599/02_2023/7k0j_22599_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.073 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 Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7683 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.04, per 1000 atoms: 0.66 Number of scatterers: 7683 At special positions: 0 Unit cell: (88.044, 81.0405, 128.064, 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 44 16.00 P 1 15.00 O 1413 8.00 N 1305 7.00 C 4920 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 6 sheets defined 44.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.536A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.062A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.692A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.615A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.923A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 5.684A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 297 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 434 through 456 removed outlier: 3.684A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.901A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 54 Processing helix chain 'C' and resid 58 through 68 Processing sheet with id= A, first strand: chain 'A' and resid 93 through 95 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.545A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= D, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.536A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.860A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2500 1.34 - 1.46: 1123 1.46 - 1.57: 4144 1.57 - 1.69: 1 1.69 - 1.81: 71 Bond restraints: 7839 Sorted by residual: bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.12e+00 bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.21e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.80e+00 bond pdb=" C ARG A 287 " pdb=" N GLY A 288 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.12e-02 7.97e+03 1.95e+00 ... (remaining 7834 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 185 106.10 - 113.09: 4185 113.09 - 120.08: 2804 120.08 - 127.07: 3345 127.07 - 134.06: 72 Bond angle restraints: 10591 Sorted by residual: angle pdb=" C GLY B 497 " pdb=" N PHE B 498 " pdb=" CA PHE B 498 " ideal model delta sigma weight residual 120.09 125.22 -5.13 1.25e+00 6.40e-01 1.68e+01 angle pdb=" C VAL A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta sigma weight residual 122.18 119.85 2.33 6.90e-01 2.10e+00 1.14e+01 angle pdb=" C LEU B 365 " pdb=" N ASP B 366 " pdb=" CA ASP B 366 " ideal model delta sigma weight residual 121.59 131.87 -10.28 3.54e+00 7.98e-02 8.44e+00 angle pdb=" CA PHE B 121 " pdb=" C PHE B 121 " pdb=" O PHE B 121 " ideal model delta sigma weight residual 121.07 117.93 3.14 1.10e+00 8.26e-01 8.17e+00 angle pdb=" C ILE B 426 " pdb=" N MET B 427 " pdb=" CA MET B 427 " ideal model delta sigma weight residual 122.65 118.00 4.65 1.66e+00 3.63e-01 7.83e+00 ... (remaining 10586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4320 17.92 - 35.85: 329 35.85 - 53.77: 56 53.77 - 71.69: 5 71.69 - 89.62: 7 Dihedral angle restraints: 4717 sinusoidal: 1894 harmonic: 2823 Sorted by residual: dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA MET C 28 " pdb=" C MET C 28 " pdb=" N LEU C 29 " pdb=" CA LEU C 29 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 451 " pdb=" CG GLU A 451 " pdb=" CD GLU A 451 " pdb=" OE1 GLU A 451 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 705 0.036 - 0.071: 320 0.071 - 0.107: 108 0.107 - 0.143: 35 0.143 - 0.178: 1 Chirality restraints: 1169 Sorted by residual: chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA LEU A 257 " pdb=" N LEU A 257 " pdb=" C LEU A 257 " pdb=" CB LEU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1166 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.016 2.00e-02 2.50e+03 1.20e-02 2.88e+00 pdb=" CG TYR A 166 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 470 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 499 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.024 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1093 2.75 - 3.29: 7101 3.29 - 3.82: 12190 3.82 - 4.36: 14673 4.36 - 4.90: 26856 Nonbonded interactions: 61913 Sorted by model distance: nonbonded pdb=" OD2 ASP A 228 " pdb=" NH2 ARG A 240 " model vdw 2.210 2.520 nonbonded pdb=" OE2 GLU A 274 " pdb=" OG SER A 276 " model vdw 2.221 2.440 nonbonded pdb=" O GLU A 67 " pdb=" OH TYR B 340 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR B 378 " pdb=" O3P PLP B 601 " model vdw 2.282 2.440 nonbonded pdb=" NH2 ARG A 270 " pdb=" OE2 GLU B 104 " model vdw 2.314 2.520 ... (remaining 61908 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 4920 2.51 5 N 1305 2.21 5 O 1413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.120 Check model and map are aligned: 0.130 Process input model: 24.200 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 7839 Z= 0.412 Angle : 0.712 10.284 10591 Z= 0.407 Chirality : 0.046 0.178 1169 Planarity : 0.004 0.041 1360 Dihedral : 13.138 89.617 2913 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.00 % 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: 0.19 (0.26), residues: 971 helix: 1.30 (0.24), residues: 444 sheet: -0.62 (0.50), residues: 113 loop : -0.92 (0.28), residues: 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.952 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2633 time to fit residues: 30.1559 Evaluate side-chains 74 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7839 Z= 0.270 Angle : 0.540 9.311 10591 Z= 0.278 Chirality : 0.042 0.136 1169 Planarity : 0.004 0.039 1360 Dihedral : 5.275 64.461 1092 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.62 % 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: 0.51 (0.26), residues: 971 helix: 1.58 (0.24), residues: 443 sheet: -0.62 (0.51), residues: 113 loop : -0.71 (0.29), residues: 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.998 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.2627 time to fit residues: 28.5474 Evaluate side-chains 80 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0762 time to fit residues: 1.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7839 Z= 0.180 Angle : 0.477 8.640 10591 Z= 0.247 Chirality : 0.040 0.135 1169 Planarity : 0.004 0.033 1360 Dihedral : 5.016 64.018 1092 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.50 % 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: 0.90 (0.27), residues: 971 helix: 1.94 (0.24), residues: 442 sheet: -0.17 (0.49), residues: 124 loop : -0.64 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.171 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 0.2718 time to fit residues: 31.0375 Evaluate side-chains 77 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0881 time to fit residues: 1.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7839 Z= 0.197 Angle : 0.481 8.326 10591 Z= 0.249 Chirality : 0.041 0.134 1169 Planarity : 0.004 0.034 1360 Dihedral : 4.909 63.677 1092 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.62 % 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: 0.96 (0.27), residues: 971 helix: 2.02 (0.25), residues: 443 sheet: -0.11 (0.48), residues: 126 loop : -0.66 (0.30), residues: 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.949 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 82 average time/residue: 0.2734 time to fit residues: 29.3138 Evaluate side-chains 79 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0786 time to fit residues: 1.5958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.0770 chunk 53 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7839 Z= 0.180 Angle : 0.461 8.110 10591 Z= 0.239 Chirality : 0.040 0.133 1169 Planarity : 0.003 0.033 1360 Dihedral : 4.819 63.747 1092 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.24 % 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 (0.27), residues: 971 helix: 2.13 (0.25), residues: 442 sheet: -0.08 (0.48), residues: 126 loop : -0.65 (0.30), residues: 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.967 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 90 average time/residue: 0.2562 time to fit residues: 30.5289 Evaluate side-chains 88 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0761 time to fit residues: 1.7971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7839 Z= 0.200 Angle : 0.470 8.360 10591 Z= 0.243 Chirality : 0.041 0.134 1169 Planarity : 0.003 0.034 1360 Dihedral : 4.808 63.855 1092 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.75 % 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: 0.99 (0.27), residues: 971 helix: 2.14 (0.25), residues: 443 sheet: -0.41 (0.52), residues: 113 loop : -0.66 (0.29), residues: 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.031 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 0.2578 time to fit residues: 31.0224 Evaluate side-chains 88 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0830 time to fit residues: 1.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.0060 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7839 Z= 0.150 Angle : 0.443 7.905 10591 Z= 0.230 Chirality : 0.040 0.134 1169 Planarity : 0.003 0.034 1360 Dihedral : 4.713 63.619 1092 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 971 helix: 2.26 (0.25), residues: 443 sheet: 0.00 (0.49), residues: 125 loop : -0.60 (0.30), residues: 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.989 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 90 average time/residue: 0.2743 time to fit residues: 32.1222 Evaluate side-chains 89 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0703 time to fit residues: 1.3437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.4980 chunk 28 optimal weight: 0.0670 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 184 ASN B 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7839 Z= 0.159 Angle : 0.444 8.159 10591 Z= 0.230 Chirality : 0.040 0.134 1169 Planarity : 0.003 0.034 1360 Dihedral : 4.669 63.385 1092 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.25 % 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: 1.25 (0.27), residues: 971 helix: 2.30 (0.25), residues: 443 sheet: 0.03 (0.49), residues: 125 loop : -0.58 (0.30), residues: 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.996 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.2656 time to fit residues: 31.8877 Evaluate side-chains 88 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7839 Z= 0.214 Angle : 0.473 8.738 10591 Z= 0.243 Chirality : 0.041 0.132 1169 Planarity : 0.003 0.035 1360 Dihedral : 4.747 63.926 1092 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 971 helix: 2.22 (0.25), residues: 442 sheet: -0.07 (0.49), residues: 126 loop : -0.63 (0.30), residues: 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.991 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.2689 time to fit residues: 30.9888 Evaluate side-chains 86 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0766 time to fit residues: 1.4570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7839 Z= 0.177 Angle : 0.454 8.417 10591 Z= 0.235 Chirality : 0.040 0.133 1169 Planarity : 0.003 0.034 1360 Dihedral : 4.715 64.025 1092 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.25 % 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: 1.20 (0.27), residues: 971 helix: 2.26 (0.25), residues: 443 sheet: -0.01 (0.49), residues: 126 loop : -0.59 (0.30), residues: 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.020 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2772 time to fit residues: 32.6594 Evaluate side-chains 87 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0837 time to fit residues: 1.5539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093298 restraints weight = 9801.818| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.45 r_work: 0.2953 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 7839 Z= 0.248 Angle : 0.490 8.823 10591 Z= 0.252 Chirality : 0.041 0.132 1169 Planarity : 0.004 0.035 1360 Dihedral : 4.810 64.411 1092 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.12 % 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: 1.07 (0.27), residues: 971 helix: 2.15 (0.24), residues: 443 sheet: -0.10 (0.48), residues: 126 loop : -0.66 (0.30), residues: 402 =============================================================================== Job complete usr+sys time: 1888.58 seconds wall clock time: 35 minutes 18.21 seconds (2118.21 seconds total)