Starting phenix.real_space_refine (version: dev) on Mon Apr 4 16:34:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_2022/7k0l_22601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0l_22601/04_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 3.10 Conformation dependent library (CDL) restraints added in 1.1 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: 0.84 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: 2.14 Time building geometry restraints manager: 3.33 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=" C20 VRP B 602 " pdb=" C23 VRP B 602 " ideal model delta sigma weight residual 1.526 1.588 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C16 VRP B 602 " pdb=" C17 VRP B 602 " ideal model delta sigma weight residual 1.561 1.499 0.062 2.00e-02 2.50e+03 9.55e+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 6.13e+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 ... (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=" C15 VRP B 602 " pdb=" C16 VRP B 602 " pdb=" C17 VRP B 602 " ideal model delta sigma weight residual 152.66 124.99 27.67 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C14 VRP B 602 " pdb=" C15 VRP B 602 " pdb=" C16 VRP B 602 " ideal model delta sigma weight residual 112.22 123.66 -11.44 3.00e+00 1.11e-01 1.45e+01 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 ... (remaining 10501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 4421 22.52 - 45.03: 229 45.03 - 67.55: 15 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 - 0.042: 864 0.042 - 0.084: 206 0.084 - 0.126: 84 0.126 - 0.168: 4 0.168 - 0.210: 1 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C20 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" C21 VRP B 602 " pdb=" C23 VRP B 602 " both_signs ideal model delta sigma weight residual False -2.76 -2.97 0.21 2.00e-01 2.50e+01 1.11e+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: 1.990 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: 11.960 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- 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 0.062 7775 Z= 0.268 Angle : 0.692 27.666 10506 Z= 0.377 Chirality : 0.042 0.210 1159 Planarity : 0.004 0.061 1348 Dihedral : 12.601 112.583 2891 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.28 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 : 0.988 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2263 time to fit residues: 20.4521 Evaluate side-chains 56 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4035 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8665 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7775 Z= 0.212 Angle : 0.480 6.599 10506 Z= 0.256 Chirality : 0.041 0.140 1159 Planarity : 0.005 0.054 1348 Dihedral : 5.472 80.603 1075 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.03 (0.27), residues: 958 helix: 1.80 (0.25), residues: 434 sheet: 0.54 (0.49), residues: 119 loop : -0.48 (0.29), residues: 405 *********************** 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 : 1.068 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.1945 time to fit residues: 15.9609 Evaluate side-chains 58 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0834 time to fit residues: 1.5390 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8701 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 7775 Z= 0.320 Angle : 0.527 7.133 10506 Z= 0.279 Chirality : 0.043 0.142 1159 Planarity : 0.005 0.054 1348 Dihedral : 5.335 76.864 1075 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.76 (0.27), residues: 958 helix: 1.56 (0.25), residues: 440 sheet: 0.46 (0.49), residues: 117 loop : -0.66 (0.28), residues: 401 *********************** 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: 6 poor density : 56 time to evaluate : 0.959 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.1809 time to fit residues: 16.3092 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0798 time to fit residues: 1.7172 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7775 Z= 0.224 Angle : 0.479 6.608 10506 Z= 0.255 Chirality : 0.041 0.138 1159 Planarity : 0.004 0.051 1348 Dihedral : 5.143 86.962 1075 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.83 (0.27), residues: 958 helix: 1.69 (0.25), residues: 434 sheet: 0.34 (0.46), residues: 133 loop : -0.65 (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 62 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.951 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.2004 time to fit residues: 17.6494 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1343 time to fit residues: 1.6119 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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: 0.8669 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7775 Z= 0.182 Angle : 0.456 6.581 10506 Z= 0.243 Chirality : 0.040 0.135 1159 Planarity : 0.004 0.049 1348 Dihedral : 4.706 72.787 1075 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.87 % 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: 0.95 (0.27), residues: 958 helix: 1.78 (0.26), residues: 434 sheet: 0.42 (0.46), residues: 133 loop : -0.58 (0.29), residues: 391 *********************** 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 67 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.977 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.1708 time to fit residues: 16.5100 Evaluate side-chains 59 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0872 time to fit residues: 1.8046 ------------------------------------------------------------------------------- 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: 0.6980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 7775 Z= 0.174 Angle : 0.445 6.577 10506 Z= 0.238 Chirality : 0.040 0.139 1159 Planarity : 0.005 0.095 1348 Dihedral : 4.451 61.030 1075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.00 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: 0.99 (0.27), residues: 958 helix: 1.84 (0.26), residues: 433 sheet: 0.42 (0.46), residues: 133 loop : -0.57 (0.30), 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 64 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.994 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 62 average time/residue: 0.1847 time to fit residues: 17.1225 Evaluate side-chains 61 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0888 time to fit residues: 1.7542 ------------------------------------------------------------------------------- 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: 0.0770 chunk 52 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7775 Z= 0.159 Angle : 0.442 6.633 10506 Z= 0.236 Chirality : 0.040 0.141 1159 Planarity : 0.004 0.076 1348 Dihedral : 4.286 52.295 1075 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.13 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: 1.06 (0.27), residues: 958 helix: 1.89 (0.26), residues: 433 sheet: 0.44 (0.46), residues: 133 loop : -0.53 (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 58 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.910 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1702 time to fit residues: 15.0395 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3139 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.8663 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7775 Z= 0.183 Angle : 0.440 6.590 10506 Z= 0.236 Chirality : 0.040 0.143 1159 Planarity : 0.004 0.071 1348 Dihedral : 4.158 43.889 1075 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.05 (0.27), residues: 958 helix: 1.90 (0.26), residues: 432 sheet: 0.41 (0.45), residues: 136 loop : -0.56 (0.30), residues: 390 *********************** 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 60 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.837 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1557 time to fit residues: 13.8955 Evaluate side-chains 58 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1038 time to fit residues: 1.3109 ------------------------------------------------------------------------------- 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: 0.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8674 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 7775 Z= 0.219 Angle : 0.471 7.742 10506 Z= 0.252 Chirality : 0.040 0.143 1159 Planarity : 0.005 0.112 1348 Dihedral : 4.170 37.799 1075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.92 (0.27), residues: 958 helix: 1.78 (0.26), residues: 437 sheet: 0.26 (0.46), residues: 135 loop : -0.61 (0.30), residues: 386 *********************** 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 62 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.978 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.1800 time to fit residues: 16.0147 Evaluate side-chains 57 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2028 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8672 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 7775 Z= 0.205 Angle : 0.459 6.836 10506 Z= 0.247 Chirality : 0.040 0.146 1159 Planarity : 0.005 0.099 1348 Dihedral : 4.090 33.059 1075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.95 (0.28), residues: 958 helix: 1.84 (0.26), residues: 431 sheet: 0.26 (0.46), residues: 135 loop : -0.58 (0.30), residues: 392 ********************** 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 58 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.991 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1937 time to fit residues: 16.6931 Evaluate side-chains 56 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2371 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084487 restraints weight = 15987.069| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.26 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3182 rms_B_bonded: 2.06 restraints_weight: 0.1250 r_work: 0.3171 rms_B_bonded: 2.13 restraints_weight: 0.0625 r_work: 0.3160 rms_B_bonded: 2.24 restraints_weight: 0.0312 r_work: 0.3148 rms_B_bonded: 2.37 restraints_weight: 0.0156 r_work: 0.3136 rms_B_bonded: 2.54 restraints_weight: 0.0078 r_work: 0.3122 rms_B_bonded: 2.73 restraints_weight: 0.0039 r_work: 0.3108 rms_B_bonded: 2.95 restraints_weight: 0.0020 r_work: 0.3092 rms_B_bonded: 3.20 restraints_weight: 0.0010 r_work: 0.3076 rms_B_bonded: 3.49 restraints_weight: 0.0005 r_work: 0.3058 rms_B_bonded: 3.82 restraints_weight: 0.0002 r_work: 0.3038 rms_B_bonded: 4.19 restraints_weight: 0.0001 r_work: 0.3017 rms_B_bonded: 4.60 restraints_weight: 0.0001 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 7775 Z= 0.217 Angle : 0.489 9.887 10506 Z= 0.261 Chirality : 0.041 0.198 1159 Planarity : 0.005 0.091 1348 Dihedral : 4.086 33.484 1075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.46 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: 0.86 (0.28), residues: 958 helix: 1.71 (0.26), residues: 438 sheet: 0.25 (0.46), residues: 135 loop : -0.61 (0.30), residues: 385 =============================================================================== Job complete usr+sys time: 1588.29 seconds wall clock time: 29 minutes 39.20 seconds (1779.20 seconds total)