Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 17:23:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozw_13139/07_2023/7ozw_13139_updated.pdb" } resolution = 3.38 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= 0.020 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 14 5.16 5 C 5341 2.51 5 N 1404 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4388 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 514} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3303 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 699 Classifications: {'DNA': 32, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'3IR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.55 Number of scatterers: 8407 At special positions: 0 Unit cell: (94.09, 99.91, 102.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 34 15.00 O 1614 8.00 N 1404 7.00 C 5341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 32.6% alpha, 13.8% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.679A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.172A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 117 No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.716A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.524A pdb=" N THR A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.822A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.753A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.688A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.984A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.633A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.946A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 395 through 401 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 removed outlier: 3.545A pdb=" N TYR A 183 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.730A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.243A pdb=" N LYS A 388 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 329 through 331 Processing sheet with id= F, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.793A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.531A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.803A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.215A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1323 1.32 - 1.44: 2426 1.44 - 1.56: 4858 1.56 - 1.69: 68 1.69 - 1.81: 26 Bond restraints: 8701 Sorted by residual: bond pdb=" C5 OMC F 2 " pdb=" C6 OMC F 2 " ideal model delta sigma weight residual 1.488 1.346 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C2 OMC F 2 " pdb=" N3 OMC F 2 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C2 OMC F 4 " pdb=" N3 OMC F 4 " ideal model delta sigma weight residual 1.491 1.351 0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" N3 OMC F 2 " pdb=" C4 OMC F 2 " ideal model delta sigma weight residual 1.448 1.317 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C4 OMC F 2 " pdb=" N4 OMC F 2 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.65e+01 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 56.83 - 72.74: 3 72.74 - 88.65: 0 88.65 - 104.56: 297 104.56 - 120.47: 8250 120.47 - 136.38: 3441 Bond angle restraints: 11991 Sorted by residual: angle pdb=" C5' DC F 10 " pdb=" C4' DC F 10 " pdb=" O4' DC F 10 " ideal model delta sigma weight residual 109.40 131.51 -22.11 1.50e+00 4.44e-01 2.17e+02 angle pdb=" C5 3IR A 601 " pdb=" C7 3IR A 601 " pdb=" C8 3IR A 601 " ideal model delta sigma weight residual 120.05 136.38 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 106.61 115.90 -9.29 1.78e+00 3.16e-01 2.73e+01 angle pdb=" C5' DG F 24 " pdb=" C4' DG F 24 " pdb=" O4' DG F 24 " ideal model delta sigma weight residual 109.40 116.21 -6.81 1.50e+00 4.44e-01 2.06e+01 angle pdb=" N TRP A 535 " pdb=" CA TRP A 535 " pdb=" C TRP A 535 " ideal model delta sigma weight residual 109.07 116.26 -7.19 1.61e+00 3.86e-01 1.99e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4395 17.89 - 35.77: 509 35.77 - 53.66: 141 53.66 - 71.55: 36 71.55 - 89.43: 11 Dihedral angle restraints: 5092 sinusoidal: 2285 harmonic: 2807 Sorted by residual: dihedral pdb=" CA VAL B 423 " pdb=" C VAL B 423 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N GLU A 36 " pdb=" CA GLU A 36 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASP B 86 " pdb=" C ASP B 86 " pdb=" N PHE B 87 " pdb=" CA PHE B 87 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1295 0.152 - 0.305: 14 0.305 - 0.457: 2 0.457 - 0.609: 0 0.609 - 0.762: 1 Chirality restraints: 1312 Sorted by residual: chirality pdb=" C4' DC F 10 " pdb=" C5' DC F 10 " pdb=" O4' DC F 10 " pdb=" C3' DC F 10 " both_signs ideal model delta sigma weight residual False -2.53 -1.76 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA PHE B 77 " pdb=" N PHE B 77 " pdb=" C PHE B 77 " pdb=" CB PHE B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C4' DG F 24 " pdb=" C5' DG F 24 " pdb=" O4' DG F 24 " pdb=" C3' DG F 24 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1309 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC F 4 " -0.038 2.00e-02 2.50e+03 5.60e-01 7.05e+03 pdb=" C4' OMC F 4 " 0.464 2.00e-02 2.50e+03 pdb=" O4' OMC F 4 " 0.659 2.00e-02 2.50e+03 pdb=" C3' OMC F 4 " -0.566 2.00e-02 2.50e+03 pdb=" O3' OMC F 4 " -0.535 2.00e-02 2.50e+03 pdb=" C2' OMC F 4 " -0.230 2.00e-02 2.50e+03 pdb=" O2' OMC F 4 " 0.858 2.00e-02 2.50e+03 pdb=" C1' OMC F 4 " 0.236 2.00e-02 2.50e+03 pdb=" N1 OMC F 4 " -0.848 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC F 2 " 0.071 2.00e-02 2.50e+03 5.60e-01 7.05e+03 pdb=" C4' OMC F 2 " 0.421 2.00e-02 2.50e+03 pdb=" O4' OMC F 2 " 0.514 2.00e-02 2.50e+03 pdb=" C3' OMC F 2 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMC F 2 " -0.598 2.00e-02 2.50e+03 pdb=" C2' OMC F 2 " -0.184 2.00e-02 2.50e+03 pdb=" O2' OMC F 2 " 0.945 2.00e-02 2.50e+03 pdb=" C1' OMC F 2 " 0.247 2.00e-02 2.50e+03 pdb=" N1 OMC F 2 " -0.823 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 312 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 313 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.040 5.00e-02 4.00e+02 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2074 2.80 - 3.33: 7534 3.33 - 3.85: 14119 3.85 - 4.38: 16396 4.38 - 4.90: 27495 Nonbonded interactions: 67618 Sorted by model distance: nonbonded pdb=" NH1 ARG A 277 " pdb=" O ALA A 355 " model vdw 2.276 2.520 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.308 2.520 nonbonded pdb=" O TYR A 427 " pdb=" NE2 GLN A 509 " model vdw 2.323 2.520 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.328 2.520 nonbonded pdb=" OG1 THR A 403 " pdb=" OE1 GLU A 404 " model vdw 2.329 2.440 ... (remaining 67613 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 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: 0.080 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: 1.280 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.210 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.007 0.142 8701 Z= 0.404 Angle : 0.829 22.106 11991 Z= 0.478 Chirality : 0.055 0.762 1312 Planarity : 0.022 0.560 1397 Dihedral : 16.906 89.432 3282 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.27), residues: 955 helix: 0.76 (0.29), residues: 326 sheet: 0.00 (0.42), residues: 126 loop : -0.83 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2622 time to fit residues: 42.2830 Evaluate side-chains 99 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8701 Z= 0.192 Angle : 0.703 13.735 11991 Z= 0.405 Chirality : 0.043 0.140 1312 Planarity : 0.006 0.120 1397 Dihedral : 17.047 82.235 1379 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 955 helix: 1.19 (0.30), residues: 326 sheet: -0.19 (0.41), residues: 137 loop : -0.59 (0.28), residues: 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.849 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 0.2349 time to fit residues: 37.7321 Evaluate side-chains 107 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0918 time to fit residues: 1.8406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 8701 Z= 0.304 Angle : 0.741 13.108 11991 Z= 0.425 Chirality : 0.044 0.145 1312 Planarity : 0.007 0.117 1397 Dihedral : 17.257 82.854 1379 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 955 helix: 0.94 (0.29), residues: 317 sheet: -0.54 (0.40), residues: 140 loop : -0.70 (0.28), residues: 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.864 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 116 average time/residue: 0.2378 time to fit residues: 37.0224 Evaluate side-chains 106 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0953 time to fit residues: 1.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8701 Z= 0.257 Angle : 0.716 13.094 11991 Z= 0.414 Chirality : 0.043 0.142 1312 Planarity : 0.006 0.114 1397 Dihedral : 17.178 83.072 1379 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 955 helix: 0.94 (0.30), residues: 316 sheet: -0.56 (0.40), residues: 138 loop : -0.78 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.047 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 119 average time/residue: 0.2456 time to fit residues: 39.7682 Evaluate side-chains 113 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0892 time to fit residues: 2.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 428 GLN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 8701 Z= 0.303 Angle : 0.741 13.065 11991 Z= 0.425 Chirality : 0.044 0.149 1312 Planarity : 0.007 0.115 1397 Dihedral : 17.168 84.694 1379 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 955 helix: 0.72 (0.29), residues: 316 sheet: -0.67 (0.41), residues: 138 loop : -0.94 (0.27), residues: 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.957 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 115 average time/residue: 0.2373 time to fit residues: 37.4484 Evaluate side-chains 107 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0818 time to fit residues: 1.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 428 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 8701 Z= 0.321 Angle : 0.759 13.242 11991 Z= 0.433 Chirality : 0.045 0.167 1312 Planarity : 0.007 0.115 1397 Dihedral : 17.293 88.431 1379 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 955 helix: 0.54 (0.29), residues: 317 sheet: -0.82 (0.43), residues: 135 loop : -1.07 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.996 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.2450 time to fit residues: 38.7028 Evaluate side-chains 114 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0850 time to fit residues: 2.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8701 Z= 0.276 Angle : 0.739 13.241 11991 Z= 0.424 Chirality : 0.044 0.155 1312 Planarity : 0.007 0.114 1397 Dihedral : 17.268 91.063 1379 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 955 helix: 0.64 (0.30), residues: 316 sheet: -0.84 (0.43), residues: 135 loop : -1.05 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 0.2407 time to fit residues: 37.3775 Evaluate side-chains 110 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0829 time to fit residues: 1.7752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.0370 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8701 Z= 0.177 Angle : 0.693 13.083 11991 Z= 0.402 Chirality : 0.042 0.138 1312 Planarity : 0.006 0.113 1397 Dihedral : 16.978 92.954 1379 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 955 helix: 1.03 (0.30), residues: 316 sheet: -0.62 (0.43), residues: 138 loop : -0.79 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.2354 time to fit residues: 37.9402 Evaluate side-chains 110 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0801 time to fit residues: 1.5633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 373 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8701 Z= 0.237 Angle : 0.720 13.026 11991 Z= 0.414 Chirality : 0.043 0.144 1312 Planarity : 0.006 0.114 1397 Dihedral : 17.076 95.739 1379 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 955 helix: 0.95 (0.30), residues: 316 sheet: -0.64 (0.43), residues: 138 loop : -0.86 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.976 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 110 average time/residue: 0.2280 time to fit residues: 34.7083 Evaluate side-chains 109 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0912 time to fit residues: 2.1232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 0.1980 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8701 Z= 0.180 Angle : 0.691 13.007 11991 Z= 0.401 Chirality : 0.042 0.137 1312 Planarity : 0.006 0.113 1397 Dihedral : 16.892 95.076 1379 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 955 helix: 1.11 (0.30), residues: 316 sheet: -0.52 (0.42), residues: 144 loop : -0.72 (0.28), residues: 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.983 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.2264 time to fit residues: 32.3257 Evaluate side-chains 103 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 0.0010 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.214020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176195 restraints weight = 9223.782| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.87 r_work: 0.3855 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8701 Z= 0.151 Angle : 0.688 12.859 11991 Z= 0.397 Chirality : 0.041 0.136 1312 Planarity : 0.006 0.113 1397 Dihedral : 16.642 93.953 1379 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 955 helix: 1.38 (0.31), residues: 311 sheet: -0.28 (0.43), residues: 142 loop : -0.63 (0.28), residues: 502 =============================================================================== Job complete usr+sys time: 1686.51 seconds wall clock time: 31 minutes 43.62 seconds (1903.62 seconds total)