Starting phenix.real_space_refine (version: dev) on Mon Dec 12 18:57:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/12_2022/7udc_26456.pdb" } resolution = 3.7 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5307 atoms to isotropic. 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 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 6425 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4331 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 27, 'TRANS': 514} Chain breaks: 3 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1716 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Time building chain proxies: 4.13, per 1000 atoms: 0.64 Number of scatterers: 6425 At special positions: 0 Unit cell: (92.88, 109.08, 91.8, 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 35 16.00 O 1268 8.00 N 1092 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS C 36 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.631A pdb=" N CYS A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.942A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.347A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.745A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 removed outlier: 3.581A pdb=" N THR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.816A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 313 removed outlier: 4.065A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLN A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 359 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 361 through 375 removed outlier: 3.893A pdb=" N ASP A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Proline residue: A 392 - end of helix removed outlier: 3.529A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.741A pdb=" N TYR A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.304A pdb=" N ILE A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.848A pdb=" N ASP A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.958A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.708A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 28 through 64 Processing helix chain 'B' and resid 68 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.132A pdb=" N ASN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 149 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 204 through 221 removed outlier: 3.849A pdb=" N GLU B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 231 removed outlier: 3.756A pdb=" N ASP B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 73 removed outlier: 4.112A pdb=" N GLU C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 removed outlier: 4.021A pdb=" N PHE C 77 " --> pdb=" O ALA C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.050A pdb=" N LYS A 29 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 57 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 76 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 32 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 73 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 105 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR A 75 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 102 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A 129 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.659A pdb=" N TYR A 145 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 537 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY A 568 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 539 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 229 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266 353 hydrogen bonds defined for protein. 1050 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: 1.94 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2154 1.34 - 1.46: 1282 1.46 - 1.58: 3018 1.58 - 1.70: 1 1.70 - 1.82: 61 Bond restraints: 6516 Sorted by residual: bond pdb=" CB PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.32e+00 bond pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.11e-01 bond pdb=" CB ASP C 65 " pdb=" CG ASP C 65 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.54e-01 bond pdb=" CA THR B 23 " pdb=" CB THR B 23 " ideal model delta sigma weight residual 1.529 1.540 -0.011 1.62e-02 3.81e+03 4.97e-01 bond pdb=" CA THR B 161 " pdb=" CB THR B 161 " ideal model delta sigma weight residual 1.540 1.521 0.019 2.70e-02 1.37e+03 4.82e-01 ... (remaining 6511 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.42: 159 106.42 - 113.32: 3647 113.32 - 120.22: 2280 120.22 - 127.13: 2642 127.13 - 134.03: 48 Bond angle restraints: 8776 Sorted by residual: angle pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" CD PRO A 223 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" CB MET A 374 " pdb=" CG MET A 374 " pdb=" SD MET A 374 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" N GLU B 73 " pdb=" CA GLU B 73 " pdb=" CB GLU B 73 " ideal model delta sigma weight residual 110.28 114.20 -3.92 1.55e+00 4.16e-01 6.39e+00 angle pdb=" C ARG A 275 " pdb=" N VAL A 276 " pdb=" CA VAL A 276 " ideal model delta sigma weight residual 121.97 126.52 -4.55 1.80e+00 3.09e-01 6.38e+00 angle pdb=" N PRO A 223 " pdb=" CD PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 103.20 99.51 3.69 1.50e+00 4.44e-01 6.04e+00 ... (remaining 8771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3646 17.89 - 35.78: 349 35.78 - 53.66: 67 53.66 - 71.55: 18 71.55 - 89.44: 5 Dihedral angle restraints: 4085 sinusoidal: 1702 harmonic: 2383 Sorted by residual: dihedral pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " pdb=" CD GLU A 66 " pdb=" OE1 GLU A 66 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN B 50 " pdb=" CB ASN B 50 " pdb=" CG ASN B 50 " pdb=" OD1 ASN B 50 " ideal model delta sinusoidal sigma weight residual -90.00 -153.56 63.56 2 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " pdb=" OD1 ASP B 27 " ideal model delta sinusoidal sigma weight residual -30.00 -83.15 53.15 1 2.00e+01 2.50e-03 9.61e+00 ... (remaining 4082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 678 0.032 - 0.064: 225 0.064 - 0.096: 76 0.096 - 0.127: 22 0.127 - 0.159: 5 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" C PRO A 223 " pdb=" CB PRO A 223 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA GLU B 73 " pdb=" N GLU B 73 " pdb=" C GLU B 73 " pdb=" CB GLU B 73 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1003 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " -0.065 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO A 223 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 369 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU A 369 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU A 369 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 78 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 79 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.022 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 512 2.74 - 3.28: 6563 3.28 - 3.82: 10244 3.82 - 4.36: 11465 4.36 - 4.90: 20211 Nonbonded interactions: 48995 Sorted by model distance: nonbonded pdb=" NZ LYS A 29 " pdb=" OE1 GLU A 72 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR A 75 " pdb=" OD2 ASP A 90 " model vdw 2.285 2.440 nonbonded pdb=" O GLN A 175 " pdb=" OG1 THR A 178 " model vdw 2.286 2.440 nonbonded pdb=" NH1 ARG A 464 " pdb=" OD2 ASP A 484 " model vdw 2.307 2.520 nonbonded pdb=" OD1 ASN A 442 " pdb=" ND2 ASN A 586 " model vdw 2.316 2.520 ... (remaining 48990 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 35 5.16 5 C 4030 2.51 5 N 1092 2.21 5 O 1268 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 20.160 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.003 0.126 6516 Z= 0.188 Angle : 0.539 8.760 8776 Z= 0.296 Chirality : 0.038 0.159 1006 Planarity : 0.004 0.096 1129 Dihedral : 14.902 89.440 2522 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.28 % 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: 1.79 (0.31), residues: 788 helix: 2.44 (0.25), residues: 447 sheet: 0.47 (0.78), residues: 54 loop : -0.74 (0.35), residues: 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.793 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1563 time to fit residues: 29.7639 Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6516 Z= 0.252 Angle : 0.515 6.680 8776 Z= 0.272 Chirality : 0.040 0.144 1006 Planarity : 0.004 0.044 1129 Dihedral : 3.588 14.548 864 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.81 % 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: 1.80 (0.30), residues: 788 helix: 2.44 (0.24), residues: 453 sheet: 0.58 (0.78), residues: 54 loop : -0.83 (0.35), residues: 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.726 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.1683 time to fit residues: 29.4500 Evaluate side-chains 114 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0588 time to fit residues: 1.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 overall best weight: 0.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6516 Z= 0.140 Angle : 0.471 6.959 8776 Z= 0.247 Chirality : 0.037 0.144 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.422 12.571 864 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.42 % 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: 1.93 (0.30), residues: 788 helix: 2.57 (0.24), residues: 456 sheet: 0.70 (0.76), residues: 55 loop : -0.87 (0.35), residues: 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.1716 time to fit residues: 27.8010 Evaluate side-chains 111 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0927 time to fit residues: 1.3686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6516 Z= 0.166 Angle : 0.471 6.822 8776 Z= 0.245 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.386 13.115 864 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 788 helix: 2.67 (0.24), residues: 454 sheet: 0.65 (0.77), residues: 54 loop : -0.83 (0.35), residues: 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.828 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.1699 time to fit residues: 26.4556 Evaluate side-chains 110 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0619 time to fit residues: 1.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6516 Z= 0.207 Angle : 0.489 6.978 8776 Z= 0.254 Chirality : 0.039 0.162 1006 Planarity : 0.003 0.037 1129 Dihedral : 3.415 14.003 864 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.83 % 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: 2.10 (0.30), residues: 788 helix: 2.74 (0.24), residues: 454 sheet: 0.58 (0.75), residues: 55 loop : -0.79 (0.35), residues: 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.792 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 119 average time/residue: 0.1741 time to fit residues: 28.0342 Evaluate side-chains 111 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0596 time to fit residues: 1.3504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 55 optimal weight: 20.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 6516 Z= 0.157 Angle : 0.469 6.343 8776 Z= 0.242 Chirality : 0.038 0.212 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.335 13.551 864 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.83 % 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: 2.17 (0.30), residues: 788 helix: 2.77 (0.24), residues: 455 sheet: 0.66 (0.77), residues: 54 loop : -0.74 (0.35), residues: 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.984 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 110 average time/residue: 0.1638 time to fit residues: 25.1822 Evaluate side-chains 109 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0680 time to fit residues: 1.7356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0040 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6516 Z= 0.145 Angle : 0.478 8.561 8776 Z= 0.242 Chirality : 0.038 0.228 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.245 11.956 864 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.30), residues: 788 helix: 2.82 (0.24), residues: 455 sheet: 0.71 (0.75), residues: 55 loop : -0.74 (0.35), residues: 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.808 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.1539 time to fit residues: 24.1827 Evaluate side-chains 105 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0655 time to fit residues: 1.3059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6516 Z= 0.221 Angle : 0.491 7.373 8776 Z= 0.253 Chirality : 0.039 0.240 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.322 14.025 864 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.30), residues: 788 helix: 2.85 (0.24), residues: 455 sheet: 0.69 (0.75), residues: 54 loop : -0.75 (0.35), residues: 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.825 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 107 average time/residue: 0.1570 time to fit residues: 23.5787 Evaluate side-chains 108 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0625 time to fit residues: 1.2451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6516 Z= 0.141 Angle : 0.470 7.137 8776 Z= 0.244 Chirality : 0.038 0.230 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.233 13.931 864 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.28 % 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: 2.32 (0.30), residues: 788 helix: 2.91 (0.24), residues: 455 sheet: 0.80 (0.76), residues: 54 loop : -0.72 (0.35), residues: 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.838 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.1617 time to fit residues: 24.2240 Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0622 time to fit residues: 1.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6516 Z= 0.156 Angle : 0.483 8.630 8776 Z= 0.246 Chirality : 0.038 0.215 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.199 14.352 864 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.42 % 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: 2.34 (0.30), residues: 788 helix: 2.93 (0.24), residues: 455 sheet: 0.74 (0.74), residues: 55 loop : -0.70 (0.36), residues: 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.839 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.1635 time to fit residues: 23.8878 Evaluate side-chains 106 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0600 time to fit residues: 1.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119010 restraints weight = 8363.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117433 restraints weight = 5653.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119577 restraints weight = 5536.898| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6516 Z= 0.172 Angle : 0.496 8.752 8776 Z= 0.258 Chirality : 0.039 0.196 1006 Planarity : 0.003 0.040 1129 Dihedral : 3.209 14.012 864 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.14 % 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: 2.35 (0.31), residues: 788 helix: 2.95 (0.24), residues: 455 sheet: 0.70 (0.74), residues: 55 loop : -0.71 (0.36), residues: 278 =============================================================================== Job complete usr+sys time: 1392.61 seconds wall clock time: 25 minutes 59.61 seconds (1559.61 seconds total)