Starting phenix.real_space_refine (version: dev) on Thu May 12 19:16:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/05_2022/7k0l_22601_updated.pdb" } resolution = 3.4 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= -0.003 sd= 0.047 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7619 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'VRP': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.66 Number of scatterers: 7619 At special positions: 0 Unit cell: (95.475, 96.48, 115.575, 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 1404 8.00 N 1293 7.00 C 4877 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 6 sheets defined 44.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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: 4.528A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (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 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' 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: 4.572A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.311A 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 362 through 377 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.704A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.612A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.284A 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 298 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' 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 433 through 456 removed outlier: 3.731A pdb=" N LYS B 436 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 437 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B 438 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.023A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (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 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 55 removed outlier: 3.542A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) 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: 3.690A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (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: 6.529A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.285A 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: 3.501A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 3.44 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: 2465 1.34 - 1.46: 1174 1.46 - 1.58: 4063 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 7775 Sorted by residual: 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 6.13e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.54e+00 bond pdb=" C18 VRP B 602 " pdb=" C19 VRP B 602 " ideal model delta sigma weight residual 1.538 1.572 -0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.12: 173 106.12 - 113.09: 4149 113.09 - 120.06: 2707 120.06 - 127.03: 3409 127.03 - 134.00: 68 Bond angle restraints: 10506 Sorted by residual: angle pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 angle pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" C ASN B 120 " ideal model delta sigma weight residual 113.16 110.18 2.98 1.24e+00 6.50e-01 5.79e+00 angle pdb=" C TYR B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.64e+00 angle pdb=" CA CYS A 133 " pdb=" C CYS A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 115.67 118.55 -2.88 1.23e+00 6.61e-01 5.50e+00 angle pdb=" CA GLU B 119 " pdb=" C GLU B 119 " pdb=" O GLU B 119 " ideal model delta sigma weight residual 120.55 118.10 2.45 1.06e+00 8.90e-01 5.34e+00 ... (remaining 10501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 4421 22.52 - 45.03: 230 45.03 - 67.55: 14 67.55 - 90.07: 3 90.07 - 112.58: 1 Dihedral angle restraints: 4669 sinusoidal: 1885 harmonic: 2784 Sorted by residual: dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -170.99 -112.58 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" CA THR B 400 " pdb=" C THR B 400 " pdb=" N HIS B 401 " pdb=" CA HIS B 401 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 80.48 -80.48 1 3.00e+01 1.11e-03 8.90e+00 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 884 0.044 - 0.087: 189 0.087 - 0.131: 82 0.131 - 0.174: 3 0.174 - 0.218: 1 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 177 " pdb=" N ASN B 177 " pdb=" C ASN B 177 " pdb=" CB ASN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-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 4.49e-01 ... (remaining 1156 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 499 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 413 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+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 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 126 2.69 - 3.24: 7435 3.24 - 3.80: 11441 3.80 - 4.35: 15090 4.35 - 4.90: 26050 Nonbonded interactions: 60142 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.141 2.440 nonbonded pdb=" OD2 ASP B 259 " pdb=" OH TYR B 318 " model vdw 2.187 2.440 nonbonded pdb=" OG SER A 401 " pdb=" OD2 ASP A 408 " model vdw 2.246 2.440 nonbonded pdb=" NE2 HIS B 263 " pdb=" O27 VRP B 602 " model vdw 2.270 2.520 nonbonded pdb=" OG1 THR A 402 " pdb=" OD1 ASP A 408 " model vdw 2.300 2.440 ... (remaining 60137 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 4877 2.51 5 N 1293 2.21 5 O 1404 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: 1.980 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: 11.950 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 25.220 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 0.034 7775 Z= 0.261 Angle : 0.601 7.474 10506 Z= 0.360 Chirality : 0.042 0.218 1159 Planarity : 0.004 0.061 1348 Dihedral : 12.593 112.583 2891 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.09 (0.27), residues: 958 helix: 1.86 (0.25), residues: 432 sheet: 0.64 (0.48), residues: 124 loop : -0.49 (0.29), residues: 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.971 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2111 time to fit residues: 19.1314 Evaluate side-chains 56 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 7775 Z= 0.260 Angle : 0.492 6.910 10506 Z= 0.265 Chirality : 0.042 0.142 1159 Planarity : 0.005 0.055 1348 Dihedral : 5.366 82.488 1075 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 958 helix: 1.66 (0.25), residues: 440 sheet: 0.50 (0.49), residues: 119 loop : -0.55 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.964 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.1887 time to fit residues: 15.5292 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 1.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8666 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7775 Z= 0.192 Angle : 0.454 6.569 10506 Z= 0.244 Chirality : 0.040 0.137 1159 Planarity : 0.004 0.053 1348 Dihedral : 4.963 76.674 1075 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.03 (0.27), residues: 958 helix: 1.80 (0.25), residues: 434 sheet: 0.52 (0.48), residues: 119 loop : -0.47 (0.29), residues: 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.992 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 0.1672 time to fit residues: 15.6503 Evaluate side-chains 55 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0784 time to fit residues: 1.6601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 91 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.8659 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7775 Z= 0.178 Angle : 0.447 6.569 10506 Z= 0.241 Chirality : 0.040 0.134 1159 Planarity : 0.005 0.088 1348 Dihedral : 4.879 86.124 1075 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.01 (0.27), residues: 958 helix: 1.84 (0.26), residues: 434 sheet: 0.43 (0.46), residues: 133 loop : -0.56 (0.29), residues: 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.937 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1720 time to fit residues: 15.4989 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1087 time to fit residues: 1.5748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 7775 Z= 0.204 Angle : 0.454 6.602 10506 Z= 0.243 Chirality : 0.040 0.133 1159 Planarity : 0.004 0.067 1348 Dihedral : 4.806 85.381 1075 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.99 (0.27), residues: 958 helix: 1.83 (0.26), residues: 434 sheet: 0.32 (0.46), residues: 135 loop : -0.54 (0.29), residues: 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.974 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 0.1742 time to fit residues: 16.0595 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0787 time to fit residues: 1.4170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 7775 Z= 0.184 Angle : 0.457 9.228 10506 Z= 0.246 Chirality : 0.040 0.179 1159 Planarity : 0.005 0.092 1348 Dihedral : 4.581 77.515 1075 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.03 (0.27), residues: 958 helix: 1.85 (0.26), residues: 433 sheet: 0.47 (0.46), residues: 133 loop : -0.54 (0.29), residues: 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.928 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.1597 time to fit residues: 15.0167 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1094 time to fit residues: 1.4573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8654 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7775 Z= 0.166 Angle : 0.452 8.288 10506 Z= 0.242 Chirality : 0.040 0.169 1159 Planarity : 0.004 0.074 1348 Dihedral : 4.371 69.904 1075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.07 (0.27), residues: 958 helix: 1.88 (0.26), residues: 433 sheet: 0.46 (0.46), residues: 133 loop : -0.50 (0.30), residues: 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.024 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1524 time to fit residues: 14.3488 Evaluate side-chains 59 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0707 time to fit residues: 1.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 7775 Z= 0.175 Angle : 0.445 7.908 10506 Z= 0.242 Chirality : 0.040 0.159 1159 Planarity : 0.005 0.100 1348 Dihedral : 4.214 62.233 1075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.08 (0.28), residues: 958 helix: 1.90 (0.26), residues: 433 sheet: 0.46 (0.46), residues: 136 loop : -0.53 (0.30), residues: 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.987 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.1575 time to fit residues: 14.9706 Evaluate side-chains 59 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0887 time to fit residues: 1.5151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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: 0.8657 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 7775 Z= 0.183 Angle : 0.456 7.632 10506 Z= 0.244 Chirality : 0.040 0.155 1159 Planarity : 0.004 0.085 1348 Dihedral : 4.106 55.053 1075 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.09 (0.28), residues: 958 helix: 1.90 (0.26), residues: 433 sheet: 0.46 (0.46), residues: 136 loop : -0.50 (0.30), residues: 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.981 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1663 time to fit residues: 15.0168 Evaluate side-chains 59 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8665 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7775 Z= 0.200 Angle : 0.456 7.518 10506 Z= 0.245 Chirality : 0.041 0.155 1159 Planarity : 0.004 0.080 1348 Dihedral : 4.031 47.299 1075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.00 (0.27), residues: 958 helix: 1.80 (0.26), residues: 439 sheet: 0.40 (0.47), residues: 126 loop : -0.52 (0.30), residues: 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.994 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.1757 time to fit residues: 15.7302 Evaluate side-chains 60 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1160 time to fit residues: 1.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081086 restraints weight = 16113.793| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.27 r_work: 0.3149 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3130 rms_B_bonded: 2.07 restraints_weight: 0.1250 r_work: 0.3119 rms_B_bonded: 2.13 restraints_weight: 0.0625 r_work: 0.3108 rms_B_bonded: 2.23 restraints_weight: 0.0312 r_work: 0.3097 rms_B_bonded: 2.36 restraints_weight: 0.0156 r_work: 0.3085 rms_B_bonded: 2.51 restraints_weight: 0.0078 r_work: 0.3072 rms_B_bonded: 2.69 restraints_weight: 0.0039 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.0020 r_work: 0.3044 rms_B_bonded: 3.13 restraints_weight: 0.0010 r_work: 0.3028 rms_B_bonded: 3.39 restraints_weight: 0.0005 r_work: 0.3011 rms_B_bonded: 3.70 restraints_weight: 0.0002 r_work: 0.2993 rms_B_bonded: 4.03 restraints_weight: 0.0001 r_work: 0.2974 rms_B_bonded: 4.41 restraints_weight: 0.0001 r_work: 0.2953 rms_B_bonded: 4.83 restraints_weight: 0.0000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 7775 Z= 0.208 Angle : 0.465 7.410 10506 Z= 0.248 Chirality : 0.041 0.154 1159 Planarity : 0.004 0.077 1348 Dihedral : 3.991 42.680 1075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.97 (0.27), residues: 958 helix: 1.77 (0.26), residues: 439 sheet: 0.37 (0.47), residues: 126 loop : -0.54 (0.30), residues: 393 =============================================================================== Job complete usr+sys time: 1555.12 seconds wall clock time: 29 minutes 6.65 seconds (1746.65 seconds total)