Starting phenix.real_space_refine (version: dev) on Tue Feb 21 02:16:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bah_15948/02_2023/8bah_15948.pdb" } resolution = 4.13 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= 0.012 sd= 0.095 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 Process input model Symmetric amino acids flipped Residue "A ASP 20": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "C PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6381 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "B" Number of atoms: 6370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6370 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 20, 'TRANS': 377} Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 920 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.82, per 1000 atoms: 0.50 Number of scatterers: 13675 At special positions: 0 Unit cell: (109.077, 84.72, 91.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 30 16.00 O 1265 8.00 N 1193 7.00 C 4382 6.00 H 6801 1.00 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: 12.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 32.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 84 removed outlier: 3.760A pdb=" N MET A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.689A pdb=" N TRP A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.123A pdb=" N VAL A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.291A pdb=" N GLY A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 68 through 84 removed outlier: 3.644A pdb=" N MET B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.134A pdb=" N ASN B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.816A pdb=" N TRP B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 275 through 280 removed outlier: 4.089A pdb=" N VAL B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 327 through 352 Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.492A pdb=" N VAL A 122 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 14 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 56 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 16 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.618A pdb=" N PHE A 211 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 212 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 242 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 241 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 263 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 252 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 265 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 5.365A pdb=" N ARG A 202 " --> pdb=" O ARG C 660 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.657A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.657A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.712A pdb=" N PHE B 211 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 241 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 263 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 252 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 265 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 163 removed outlier: 6.405A pdb=" N ILE B 162 " --> pdb=" O THR B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.643A pdb=" N PHE B 308 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG B 366 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU B 310 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP B 368 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 312 " --> pdb=" O ASP B 368 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 612 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: 5.02 Time building geometry restraints manager: 12.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6789 1.03 - 1.23: 12 1.23 - 1.42: 2960 1.42 - 1.61: 4022 1.61 - 1.81: 48 Bond restraints: 13831 Sorted by residual: bond pdb=" N ASN C 666 " pdb=" CA ASN C 666 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.62e+00 bond pdb=" N SER C 669 " pdb=" CA SER C 669 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N THR C 668 " pdb=" CA THR C 668 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.22e-02 6.72e+03 7.46e+00 bond pdb=" N HIS B 247 " pdb=" CA HIS B 247 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.67e+00 bond pdb=" CA SER B 119 " pdb=" CB SER B 119 " ideal model delta sigma weight residual 1.532 1.494 0.039 1.53e-02 4.27e+03 6.35e+00 ... (remaining 13826 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 1730 107.13 - 113.84: 14898 113.84 - 120.55: 4708 120.55 - 127.27: 3604 127.27 - 133.98: 87 Bond angle restraints: 25027 Sorted by residual: angle pdb=" CA SER B 119 " pdb=" C SER B 119 " pdb=" O SER B 119 " ideal model delta sigma weight residual 119.41 114.41 5.00 1.13e+00 7.83e-01 1.96e+01 angle pdb=" C SER B 119 " pdb=" CA SER B 119 " pdb=" CB SER B 119 " ideal model delta sigma weight residual 109.24 115.64 -6.40 1.75e+00 3.27e-01 1.34e+01 angle pdb=" CA ASN C 666 " pdb=" C ASN C 666 " pdb=" O ASN C 666 " ideal model delta sigma weight residual 121.50 117.02 4.48 1.25e+00 6.40e-01 1.28e+01 angle pdb=" CA SER C 669 " pdb=" C SER C 669 " pdb=" O SER C 669 " ideal model delta sigma weight residual 121.16 117.39 3.77 1.12e+00 7.97e-01 1.13e+01 angle pdb=" CA SER C 667 " pdb=" C SER C 667 " pdb=" O SER C 667 " ideal model delta sigma weight residual 120.51 115.75 4.76 1.43e+00 4.89e-01 1.11e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 5141 13.63 - 27.26: 288 27.26 - 40.88: 90 40.88 - 54.51: 26 54.51 - 68.14: 11 Dihedral angle restraints: 5556 sinusoidal: 2588 harmonic: 2968 Sorted by residual: dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -88.46 58.46 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP B 235 " pdb=" CB ASP B 235 " pdb=" CG ASP B 235 " pdb=" OD1 ASP B 235 " ideal model delta sinusoidal sigma weight residual -30.00 -85.44 55.44 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA CYS A 83 " pdb=" CB CYS A 83 " pdb=" SG CYS A 83 " pdb=" HG CYS A 83 " ideal model delta sinusoidal sigma weight residual -60.00 -107.89 47.89 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 864 0.051 - 0.102: 119 0.102 - 0.153: 50 0.153 - 0.204: 0 0.204 - 0.255: 2 Chirality restraints: 1035 Sorted by residual: chirality pdb=" CA SER B 119 " pdb=" N SER B 119 " pdb=" C SER B 119 " pdb=" CB SER B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA VAL C 663 " pdb=" N VAL C 663 " pdb=" C VAL C 663 " pdb=" CB VAL C 663 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA THR C 668 " pdb=" N THR C 668 " pdb=" C THR C 668 " pdb=" CB THR C 668 " both_signs ideal model delta sigma weight residual False 2.53 2.67 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1032 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 660 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ARG C 660 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 660 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 661 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 247 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C HIS B 247 " -0.046 2.00e-02 2.50e+03 pdb=" O HIS B 247 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 248 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 664 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE C 664 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 664 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 665 " 0.010 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 404 2.11 - 2.73: 25068 2.73 - 3.36: 39252 3.36 - 3.98: 49819 3.98 - 4.60: 78278 Nonbonded interactions: 192821 Sorted by model distance: nonbonded pdb=" H ASN B 110 " pdb=" OD1 ASN B 151 " model vdw 1.489 1.850 nonbonded pdb=" OD1 ASP A 9 " pdb=" HG1 THR A 12 " model vdw 1.508 1.850 nonbonded pdb=" O SER A 68 " pdb=" HG1 THR A 71 " model vdw 1.516 1.850 nonbonded pdb=" OE2 GLU B 27 " pdb=" HZ3 LYS B 70 " model vdw 1.527 1.850 nonbonded pdb=" O CYS B 139 " pdb=" H ASP B 142 " model vdw 1.534 1.850 ... (remaining 192816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 4 through 400 or resid 801 through 802)) selection = chain 'B' } 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 S 30 5.16 5 C 4382 2.51 5 N 1193 2.21 5 O 1265 1.98 5 H 6801 0.53 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: 0.570 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: 0.180 Extract box with map and model: 2.530 Check model and map are aligned: 0.200 Process input model: 46.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 0.039 7030 Z= 0.217 Angle : 0.537 6.397 9497 Z= 0.316 Chirality : 0.043 0.255 1035 Planarity : 0.004 0.036 1246 Dihedral : 10.657 68.141 2632 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 849 helix: 1.70 (0.37), residues: 205 sheet: -0.48 (0.39), residues: 169 loop : 0.29 (0.28), residues: 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3984 time to fit residues: 102.9859 Evaluate side-chains 151 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 7030 Z= 0.320 Angle : 0.545 4.014 9497 Z= 0.298 Chirality : 0.043 0.161 1035 Planarity : 0.004 0.037 1246 Dihedral : 4.677 15.710 908 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 849 helix: 1.55 (0.37), residues: 206 sheet: -0.76 (0.37), residues: 181 loop : -0.06 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3376 time to fit residues: 79.0092 Evaluate side-chains 141 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7030 Z= 0.229 Angle : 0.494 5.598 9497 Z= 0.264 Chirality : 0.042 0.143 1035 Planarity : 0.004 0.036 1246 Dihedral : 4.526 14.835 908 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 849 helix: 1.65 (0.37), residues: 212 sheet: -0.82 (0.38), residues: 169 loop : -0.14 (0.28), residues: 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3427 time to fit residues: 80.3923 Evaluate side-chains 142 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 7030 Z= 0.267 Angle : 0.508 4.160 9497 Z= 0.272 Chirality : 0.042 0.139 1035 Planarity : 0.004 0.036 1246 Dihedral : 4.608 15.823 908 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 849 helix: 1.60 (0.37), residues: 213 sheet: -0.84 (0.38), residues: 186 loop : -0.25 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3524 time to fit residues: 80.7725 Evaluate side-chains 132 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7030 Z= 0.320 Angle : 0.539 4.519 9497 Z= 0.292 Chirality : 0.042 0.157 1035 Planarity : 0.004 0.036 1246 Dihedral : 4.818 16.426 908 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 849 helix: 1.45 (0.37), residues: 211 sheet: -1.09 (0.38), residues: 187 loop : -0.47 (0.29), residues: 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3389 time to fit residues: 75.3689 Evaluate side-chains 140 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7030 Z= 0.152 Angle : 0.465 4.915 9497 Z= 0.244 Chirality : 0.043 0.143 1035 Planarity : 0.003 0.035 1246 Dihedral : 4.428 14.795 908 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 849 helix: 1.77 (0.37), residues: 213 sheet: -0.87 (0.37), residues: 186 loop : -0.32 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3621 time to fit residues: 82.4632 Evaluate side-chains 138 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7030 Z= 0.201 Angle : 0.477 5.299 9497 Z= 0.252 Chirality : 0.042 0.142 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.409 15.383 908 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 849 helix: 1.87 (0.37), residues: 213 sheet: -0.86 (0.37), residues: 186 loop : -0.39 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3268 time to fit residues: 72.0118 Evaluate side-chains 132 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 7030 Z= 0.293 Angle : 0.524 4.405 9497 Z= 0.283 Chirality : 0.042 0.155 1035 Planarity : 0.004 0.037 1246 Dihedral : 4.660 16.785 908 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 849 helix: 1.70 (0.37), residues: 213 sheet: -1.07 (0.38), residues: 186 loop : -0.58 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3360 time to fit residues: 72.6432 Evaluate side-chains 132 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 7030 Z= 0.250 Angle : 0.506 4.542 9497 Z= 0.269 Chirality : 0.042 0.151 1035 Planarity : 0.004 0.037 1246 Dihedral : 4.618 16.236 908 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 849 helix: 1.70 (0.37), residues: 212 sheet: -1.15 (0.37), residues: 186 loop : -0.65 (0.29), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3318 time to fit residues: 71.0747 Evaluate side-chains 126 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 0.0270 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 7030 Z= 0.150 Angle : 0.466 4.226 9497 Z= 0.243 Chirality : 0.042 0.145 1035 Planarity : 0.003 0.036 1246 Dihedral : 4.303 15.021 908 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 849 helix: 2.00 (0.37), residues: 212 sheet: -0.92 (0.38), residues: 186 loop : -0.51 (0.29), residues: 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3370 time to fit residues: 73.9447 Evaluate side-chains 135 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3818 r_free = 0.3818 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.090222 restraints weight = 46302.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094851 restraints weight = 22277.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097907 restraints weight = 14269.604| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 7030 Z= 0.280 Angle : 0.516 4.209 9497 Z= 0.278 Chirality : 0.042 0.151 1035 Planarity : 0.004 0.036 1246 Dihedral : 4.567 16.456 908 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 849 helix: 1.88 (0.37), residues: 212 sheet: -1.10 (0.38), residues: 186 loop : -0.63 (0.29), residues: 451 =============================================================================== Job complete usr+sys time: 3424.66 seconds wall clock time: 61 minutes 14.37 seconds (3674.37 seconds total)