Starting phenix.real_space_refine (version: dev) on Mon Apr 4 12:43:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/04_2022/6u2k_20621_neut.pdb" } resolution = 2.93 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= 0.031 sd= 0.579 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 "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4719 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4, 'peptide': 604} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 33, 'TRANS': 569, None: 4, 'PCIS': 1} Not linked: pdbres="HIS B 614 " pdbres="NAG B 701 " Not linked: pdbres="NAG B 701 " pdbres="NAG B 702 " Not linked: pdbres="NAG B 702 " pdbres="NAG B 703 " Not linked: pdbres="NAG B 703 " pdbres="NAG B 704 " Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 3.18, per 1000 atoms: 0.67 Number of scatterers: 4719 At special positions: 0 Unit cell: (96.46, 75.26, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 912 8.00 N 802 7.00 C 2979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 545 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 701 " - " NAG B 702 " " NAG B 703 " - " NAG B 704 " NAG-ASN " NAG B 701 " - " ASN B 168 " " NAG B 703 " - " ASN B 252 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 639.3 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 19.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.047A pdb=" N CYS B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.619A pdb=" N THR B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.583A pdb=" N THR B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.656A pdb=" N LYS B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.726A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.994A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.719A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 297 removed outlier: 3.615A pdb=" N ILE B 297 " --> pdb=" O HIS B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 309 through 327 removed outlier: 3.795A pdb=" N LYS B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.535A pdb=" N MET B 42 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 40 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.858A pdb=" N ALA B 194 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 190 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 189 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 291 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY B 195 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 285 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.741A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 258 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 201 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 256 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 203 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 414 removed outlier: 3.897A pdb=" N TYR B 413 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 427 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB1, first strand: chain 'B' and resid 501 through 505 removed outlier: 5.504A pdb=" N CYS B 545 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 504 " --> pdb=" O SER B 543 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 543 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 542 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.561A pdb=" N ASN B 582 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 587 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 599 " --> pdb=" O ILE B 590 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 306 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: 1.31 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1497 1.34 - 1.46: 1046 1.46 - 1.58: 2244 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 4823 Sorted by residual: bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CB VAL B 310 " pdb=" CG1 VAL B 310 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" CB VAL B 142 " pdb=" CG1 VAL B 142 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 bond pdb=" CB PRO B 563 " pdb=" CG PRO B 563 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.61e+00 bond pdb=" CG LEU B 150 " pdb=" CD1 LEU B 150 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 ... (remaining 4818 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.45: 93 104.45 - 111.88: 2221 111.88 - 119.31: 1737 119.31 - 126.73: 2436 126.73 - 134.16: 69 Bond angle restraints: 6556 Sorted by residual: angle pdb=" CA TYR B 50 " pdb=" CB TYR B 50 " pdb=" CG TYR B 50 " ideal model delta sigma weight residual 113.90 122.23 -8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C HIS B 403 " pdb=" N LEU B 404 " pdb=" CA LEU B 404 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ARG B 375 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C PHE B 480 " pdb=" N GLU B 481 " pdb=" CA GLU B 481 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N PHE B 327 " pdb=" CA PHE B 327 " pdb=" C PHE B 327 " ideal model delta sigma weight residual 110.53 105.83 4.70 1.32e+00 5.74e-01 1.27e+01 ... (remaining 6551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 2739 14.88 - 29.76: 125 29.76 - 44.64: 31 44.64 - 59.52: 5 59.52 - 74.40: 4 Dihedral angle restraints: 2904 sinusoidal: 1158 harmonic: 1746 Sorted by residual: dihedral pdb=" CA VAL B 402 " pdb=" C VAL B 402 " pdb=" N HIS B 403 " pdb=" CA HIS B 403 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA VAL B 135 " pdb=" C VAL B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO B 396 " pdb=" C PRO B 396 " pdb=" N SER B 397 " pdb=" CA SER B 397 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 2901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 387 0.042 - 0.083: 242 0.083 - 0.125: 83 0.125 - 0.166: 30 0.166 - 0.208: 7 Chirality restraints: 749 Sorted by residual: chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB THR B 552 " pdb=" CA THR B 552 " pdb=" OG1 THR B 552 " pdb=" CG2 THR B 552 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 746 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 404 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU B 404 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU B 404 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 405 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 330 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO B 331 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 480 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C PHE B 480 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 480 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 481 " 0.014 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1667 2.86 - 3.37: 3987 3.37 - 3.88: 7168 3.88 - 4.39: 8323 4.39 - 4.90: 14511 Nonbonded interactions: 35656 Sorted by model distance: nonbonded pdb=" OG SER B 248 " pdb=" OD1 ASN B 252 " model vdw 2.354 2.440 nonbonded pdb=" ND2 ASN B 387 " pdb=" O SER B 394 " model vdw 2.359 2.520 nonbonded pdb=" O TYR B 325 " pdb=" OG1 THR B 329 " model vdw 2.387 2.440 nonbonded pdb=" O CYS B 507 " pdb=" NZ LYS B 523 " model vdw 2.397 2.520 nonbonded pdb=" ND2 ASN B 414 " pdb=" O HIS B 415 " model vdw 2.428 2.520 ... (remaining 35651 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2979 2.51 5 N 802 2.21 5 O 912 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: 0.230 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: 1.620 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.030 Process input model: 17.180 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.010 0.074 4823 Z= 0.650 Angle : 0.980 8.704 6556 Z= 0.543 Chirality : 0.061 0.208 749 Planarity : 0.008 0.078 853 Dihedral : 10.029 74.405 1754 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -4.70 (0.27), residues: 598 helix: -4.66 (0.16), residues: 119 sheet: -2.91 (0.40), residues: 113 loop : -2.72 (0.27), residues: 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.8085 time to fit residues: 119.1557 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 52 ASN B 80 ASN B 109 ASN B 255 ASN B 370 GLN B 387 ASN B 414 ASN B 489 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4823 Z= 0.196 Angle : 0.596 6.617 6556 Z= 0.321 Chirality : 0.045 0.160 749 Planarity : 0.006 0.058 853 Dihedral : 5.729 21.821 667 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.91 (0.29), residues: 598 helix: -3.35 (0.32), residues: 124 sheet: -2.87 (0.39), residues: 117 loop : -2.24 (0.29), residues: 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.7390 time to fit residues: 85.3385 Evaluate side-chains 104 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 0.0914 time to fit residues: 1.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 0.0370 overall best weight: 0.5662 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4823 Z= 0.178 Angle : 0.554 8.060 6556 Z= 0.296 Chirality : 0.043 0.177 749 Planarity : 0.005 0.047 853 Dihedral : 5.306 20.472 667 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.32 (0.30), residues: 598 helix: -2.25 (0.42), residues: 123 sheet: -2.59 (0.39), residues: 126 loop : -2.04 (0.30), residues: 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 0.7948 time to fit residues: 85.2060 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.5216 time to fit residues: 3.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6516 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 4823 Z= 0.201 Angle : 0.579 9.684 6556 Z= 0.305 Chirality : 0.044 0.202 749 Planarity : 0.005 0.041 853 Dihedral : 5.208 21.551 667 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.08 (0.31), residues: 598 helix: -1.86 (0.44), residues: 123 sheet: -2.47 (0.39), residues: 126 loop : -1.96 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.565 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.7262 time to fit residues: 76.4790 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.0885 time to fit residues: 1.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 23 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 4823 Z= 0.188 Angle : 0.558 8.597 6556 Z= 0.295 Chirality : 0.044 0.153 749 Planarity : 0.005 0.097 853 Dihedral : 5.152 20.654 667 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.88 (0.31), residues: 598 helix: -1.54 (0.44), residues: 130 sheet: -2.33 (0.39), residues: 125 loop : -1.90 (0.31), residues: 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 102 average time/residue: 0.7207 time to fit residues: 78.1899 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.0966 time to fit residues: 1.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4823 Z= 0.224 Angle : 0.582 8.347 6556 Z= 0.305 Chirality : 0.044 0.157 749 Planarity : 0.005 0.069 853 Dihedral : 5.202 22.220 667 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.68 (0.32), residues: 598 helix: -1.24 (0.45), residues: 130 sheet: -2.07 (0.39), residues: 129 loop : -1.87 (0.32), residues: 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.554 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.7525 time to fit residues: 73.5394 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.0997 time to fit residues: 1.4519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 358 ASN B 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 4823 Z= 0.211 Angle : 0.592 8.736 6556 Z= 0.305 Chirality : 0.044 0.154 749 Planarity : 0.004 0.061 853 Dihedral : 5.157 20.874 667 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.52 (0.32), residues: 598 helix: -0.94 (0.46), residues: 130 sheet: -2.06 (0.40), residues: 116 loop : -1.84 (0.32), residues: 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.581 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 0.7697 time to fit residues: 79.0689 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.1894 time to fit residues: 2.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 23 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 203 HIS B 358 ASN B 489 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4823 Z= 0.173 Angle : 0.556 9.167 6556 Z= 0.287 Chirality : 0.043 0.155 749 Planarity : 0.004 0.057 853 Dihedral : 5.019 20.794 667 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.34 (0.32), residues: 598 helix: -0.69 (0.46), residues: 130 sheet: -2.10 (0.38), residues: 127 loop : -1.67 (0.33), residues: 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.529 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 95 average time/residue: 0.8292 time to fit residues: 83.2721 Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1046 time to fit residues: 1.3351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 39 optimal weight: 0.0170 chunk 59 optimal weight: 0.2980 chunk 55 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 4823 Z= 0.147 Angle : 0.563 10.412 6556 Z= 0.283 Chirality : 0.042 0.157 749 Planarity : 0.004 0.056 853 Dihedral : 4.813 19.629 667 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.02 (0.33), residues: 598 helix: -0.21 (0.48), residues: 128 sheet: -1.87 (0.39), residues: 127 loop : -1.58 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.588 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.7947 time to fit residues: 81.7146 Evaluate side-chains 91 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.3324 time to fit residues: 2.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.0270 chunk 14 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.117 4823 Z= 0.219 Angle : 0.579 9.734 6556 Z= 0.296 Chirality : 0.043 0.183 749 Planarity : 0.006 0.130 853 Dihedral : 4.815 20.543 667 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.00 (0.33), residues: 598 helix: -0.18 (0.48), residues: 130 sheet: -1.87 (0.39), residues: 127 loop : -1.56 (0.32), residues: 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.569 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 0.7883 time to fit residues: 75.2172 Evaluate side-chains 91 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1307 time to fit residues: 1.1531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111727 restraints weight = 5830.092| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.80 r_work: 0.3297 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work: 0.3274 rms_B_bonded: 2.59 restraints_weight: 0.1250 r_work: 0.3263 rms_B_bonded: 2.62 restraints_weight: 0.0625 r_work: 0.3251 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.3238 rms_B_bonded: 2.77 restraints_weight: 0.0156 r_work: 0.3225 rms_B_bonded: 2.87 restraints_weight: 0.0078 r_work: 0.3212 rms_B_bonded: 2.98 restraints_weight: 0.0039 r_work: 0.3198 rms_B_bonded: 3.12 restraints_weight: 0.0020 r_work: 0.3183 rms_B_bonded: 3.28 restraints_weight: 0.0010 r_work: 0.3168 rms_B_bonded: 3.46 restraints_weight: 0.0005 r_work: 0.3152 rms_B_bonded: 3.66 restraints_weight: 0.0002 r_work: 0.3135 rms_B_bonded: 3.89 restraints_weight: 0.0001 r_work: 0.3117 rms_B_bonded: 4.14 restraints_weight: 0.0001 r_work: 0.3097 rms_B_bonded: 4.42 restraints_weight: 0.0000 r_work: 0.3077 rms_B_bonded: 4.74 restraints_weight: 0.0000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.139 4823 Z= 0.265 Angle : 0.620 11.570 6556 Z= 0.317 Chirality : 0.044 0.150 749 Planarity : 0.006 0.144 853 Dihedral : 4.871 21.594 667 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.93 (0.33), residues: 598 helix: -0.02 (0.49), residues: 127 sheet: -1.90 (0.38), residues: 139 loop : -1.48 (0.33), residues: 332 =============================================================================== Job complete usr+sys time: 2035.74 seconds wall clock time: 36 minutes 47.15 seconds (2207.15 seconds total)