Starting phenix.real_space_refine on Fri Jul 19 14:57:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/07_2024/8jlc_36392.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5291 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "B TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B GLU 1203": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.27, per 1000 atoms: 0.64 Number of scatterers: 8189 At special positions: 0 Unit cell: (87.98, 85.49, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1489 8.00 N 1362 7.00 C 5291 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG F 1 " - " ASN A 573 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 44.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 4.099A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.316A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.965A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.911A pdb=" N PHE A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.319A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.525A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.766A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.802A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.754A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.577A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 593 through 623 Proline residue: A 610 - end of helix removed outlier: 5.245A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 removed outlier: 3.678A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.720A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 3.567A pdb=" N PHE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.760A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1210 through 1215 removed outlier: 4.235A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY B1215 " --> pdb=" O PRO B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 492 current: chain 'A' and resid 515 through 527 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'B' and resid 1142 through 1144 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.590A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 887 through 890 current: chain 'B' and resid 914 through 916 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 916 current: chain 'B' and resid 1015 through 1021 removed outlier: 4.000A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA4, first strand: chain 'B' and resid 962 through 966 removed outlier: 6.724A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA6, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AA7, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.119A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1194 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.387A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.558A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.950A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1771 1.33 - 1.47: 3037 1.47 - 1.61: 3497 1.61 - 1.75: 3 1.75 - 1.89: 75 Bond restraints: 8383 Sorted by residual: bond pdb=" C GLY A 591 " pdb=" N GLU A 592 " ideal model delta sigma weight residual 1.335 1.458 -0.123 1.35e-02 5.49e+03 8.37e+01 bond pdb=" C5 UKX A 803 " pdb=" C6 UKX A 803 " ideal model delta sigma weight residual 1.533 1.709 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C GLY A 604 " pdb=" O GLY A 604 " ideal model delta sigma weight residual 1.233 1.290 -0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 1.458 1.517 -0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C VAL A 171 " pdb=" O VAL A 171 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.13e-02 7.83e+03 1.82e+01 ... (remaining 8378 not shown) Histogram of bond angle deviations from ideal: 92.98 - 101.68: 27 101.68 - 110.37: 1815 110.37 - 119.07: 4940 119.07 - 127.77: 4486 127.77 - 136.47: 67 Bond angle restraints: 11335 Sorted by residual: angle pdb=" C GLY A 591 " pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 120.60 136.47 -15.87 1.60e+00 3.91e-01 9.84e+01 angle pdb=" OD1 ASN A 498 " pdb=" CG ASN A 498 " pdb=" ND2 ASN A 498 " ideal model delta sigma weight residual 122.60 116.64 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" N VAL A 671 " pdb=" CA VAL A 671 " pdb=" C VAL A 671 " ideal model delta sigma weight residual 110.62 115.27 -4.65 1.02e+00 9.61e-01 2.08e+01 angle pdb=" CA ASP B1256 " pdb=" CB ASP B1256 " pdb=" CG ASP B1256 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE B1148 " pdb=" CA ILE B1148 " pdb=" C ILE B1148 " ideal model delta sigma weight residual 111.62 108.13 3.49 7.90e-01 1.60e+00 1.95e+01 ... (remaining 11330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 4439 15.69 - 31.38: 423 31.38 - 47.07: 75 47.07 - 62.76: 15 62.76 - 78.45: 12 Dihedral angle restraints: 4964 sinusoidal: 2041 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N MET B1054 " pdb=" CA MET B1054 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU B1210 " pdb=" C GLU B1210 " pdb=" N ILE B1211 " pdb=" CA ILE B1211 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 1237 0.252 - 0.504: 6 0.504 - 0.755: 0 0.755 - 1.007: 0 1.007 - 1.259: 1 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C1 FUC F 3 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 3 " pdb=" O5 FUC F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.32e+01 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.67e+01 ... (remaining 1241 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.067 2.00e-02 2.50e+03 5.61e-02 7.88e+01 pdb=" CG TRP A 467 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.076 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 548 " 0.066 2.00e-02 2.50e+03 7.39e-02 6.82e+01 pdb=" CG ASN A 548 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 548 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 548 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.073 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" C7 NAG A 802 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.098 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.011 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 613 2.74 - 3.28: 8249 3.28 - 3.82: 13731 3.82 - 4.36: 16864 4.36 - 4.90: 28701 Nonbonded interactions: 68158 Sorted by model distance: nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.195 2.520 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.228 2.440 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.272 2.520 nonbonded pdb=" OD1 ASP A 470 " pdb=" NH2 ARG A 473 " model vdw 2.288 2.520 ... (remaining 68153 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: 2.110 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.580 Find NCS groups from input model: 0.080 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.011 0.176 8383 Z= 0.703 Angle : 1.185 15.868 11335 Z= 0.775 Chirality : 0.086 1.259 1244 Planarity : 0.011 0.149 1428 Dihedral : 13.035 78.450 3098 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.12 (0.26), residues: 1006 helix: 1.06 (0.25), residues: 405 sheet: -0.08 (0.33), residues: 241 loop : -1.33 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.012 TRP A 467 HIS 0.013 0.004 HIS A 161 PHE 0.068 0.011 PHE A 299 TYR 0.053 0.009 TYR A 169 ARG 0.024 0.003 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (mtp85) REVERT: A 197 MET cc_start: 0.6566 (mtm) cc_final: 0.5263 (tpt) REVERT: A 227 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (m-30) REVERT: A 366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6283 (mttm) REVERT: A 372 MET cc_start: 0.7261 (mtm) cc_final: 0.7027 (mmm) REVERT: A 444 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6245 (ttt180) REVERT: A 491 ARG cc_start: 0.7519 (tmt170) cc_final: 0.7252 (tmt170) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7509 (tmm-80) REVERT: A 542 SER cc_start: 0.8059 (t) cc_final: 0.7844 (t) REVERT: A 563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7196 (tp30) REVERT: A 567 VAL cc_start: 0.7421 (t) cc_final: 0.7180 (t) REVERT: A 568 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (p0) REVERT: A 581 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 910 ASP cc_start: 0.5165 (t0) cc_final: 0.4352 (t0) REVERT: B 925 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 1097 LEU cc_start: 0.6800 (mm) cc_final: 0.6475 (tt) REVERT: B 1127 ASN cc_start: 0.8545 (m-40) cc_final: 0.8332 (p0) REVERT: B 1203 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4936 (mm-30) REVERT: B 1219 GLN cc_start: 0.7566 (pt0) cc_final: 0.6767 (pt0) REVERT: B 1246 ASP cc_start: 0.7038 (p0) cc_final: 0.6682 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.2664 time to fit residues: 235.6807 Evaluate side-chains 131 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 434 ASN A 513 ASN B1073 ASN B1115 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8383 Z= 0.178 Angle : 0.561 8.121 11335 Z= 0.296 Chirality : 0.045 0.452 1244 Planarity : 0.003 0.034 1428 Dihedral : 6.206 56.086 1221 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 9.44 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.70 (0.27), residues: 1006 helix: 1.98 (0.25), residues: 408 sheet: 0.31 (0.34), residues: 226 loop : -1.18 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 300 HIS 0.004 0.001 HIS A 494 PHE 0.017 0.001 PHE A 512 TYR 0.013 0.001 TYR A 306 ARG 0.005 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5955 (tpp80) cc_final: 0.5707 (mtp85) REVERT: A 146 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7724 (tm-30) REVERT: A 197 MET cc_start: 0.6331 (mtm) cc_final: 0.5801 (ttm) REVERT: A 227 ASP cc_start: 0.7929 (m-30) cc_final: 0.7318 (m-30) REVERT: A 366 LYS cc_start: 0.6247 (mtmt) cc_final: 0.6015 (mttm) REVERT: A 372 MET cc_start: 0.7299 (mtm) cc_final: 0.7046 (mmm) REVERT: A 379 ASP cc_start: 0.5988 (m-30) cc_final: 0.5784 (m-30) REVERT: A 444 ARG cc_start: 0.6056 (ttp-110) cc_final: 0.5793 (ttt180) REVERT: A 491 ARG cc_start: 0.7406 (tmt170) cc_final: 0.7061 (tpt-90) REVERT: A 497 PHE cc_start: 0.6684 (m-80) cc_final: 0.6476 (m-10) REVERT: A 520 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7542 (tpt170) REVERT: A 522 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7178 (tppt) REVERT: A 563 GLU cc_start: 0.8182 (pt0) cc_final: 0.7289 (tp30) REVERT: A 567 VAL cc_start: 0.7559 (t) cc_final: 0.7345 (m) REVERT: A 619 MET cc_start: 0.7264 (mmt) cc_final: 0.7031 (mmt) REVERT: B 910 ASP cc_start: 0.5166 (t0) cc_final: 0.4668 (t0) REVERT: B 1021 ASN cc_start: 0.6648 (m-40) cc_final: 0.6285 (m-40) REVERT: B 1061 ARG cc_start: 0.6383 (mtm-85) cc_final: 0.6075 (ptp-170) REVERT: B 1219 GLN cc_start: 0.7284 (pt0) cc_final: 0.6947 (pt0) outliers start: 19 outliers final: 7 residues processed: 150 average time/residue: 1.1751 time to fit residues: 187.7215 Evaluate side-chains 130 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1146 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 62 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 378 HIS A 387 HIS ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8383 Z= 0.331 Angle : 0.612 7.930 11335 Z= 0.321 Chirality : 0.048 0.437 1244 Planarity : 0.003 0.034 1428 Dihedral : 6.070 56.505 1221 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.19 % Allowed : 12.51 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.26), residues: 1006 helix: 1.68 (0.25), residues: 412 sheet: 0.32 (0.34), residues: 231 loop : -1.15 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1014 HIS 0.005 0.001 HIS A 387 PHE 0.016 0.002 PHE A 640 TYR 0.021 0.002 TYR A 306 ARG 0.006 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5968 (tpp80) cc_final: 0.5701 (mtp85) REVERT: A 146 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7684 (tm-30) REVERT: A 197 MET cc_start: 0.6214 (mtm) cc_final: 0.5085 (tpt) REVERT: A 252 VAL cc_start: 0.5815 (OUTLIER) cc_final: 0.5559 (p) REVERT: A 301 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: A 366 LYS cc_start: 0.6389 (mtmt) cc_final: 0.6152 (mttm) REVERT: A 372 MET cc_start: 0.7252 (mtm) cc_final: 0.6970 (mmp) REVERT: A 379 ASP cc_start: 0.5944 (m-30) cc_final: 0.5741 (m-30) REVERT: A 444 ARG cc_start: 0.6112 (ttp-110) cc_final: 0.5756 (ttt90) REVERT: A 491 ARG cc_start: 0.7426 (tmt170) cc_final: 0.7097 (tpt-90) REVERT: A 520 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7482 (tpt170) REVERT: A 522 LYS cc_start: 0.7364 (ttpt) cc_final: 0.7157 (tppt) REVERT: A 563 GLU cc_start: 0.8234 (pt0) cc_final: 0.7395 (tp30) REVERT: A 567 VAL cc_start: 0.7683 (t) cc_final: 0.7433 (m) REVERT: A 742 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 910 ASP cc_start: 0.5306 (t0) cc_final: 0.5028 (t0) REVERT: B 1061 ARG cc_start: 0.6327 (mtm-85) cc_final: 0.6018 (ptp-170) REVERT: B 1097 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5883 (tt) outliers start: 28 outliers final: 14 residues processed: 153 average time/residue: 1.2350 time to fit residues: 200.5211 Evaluate side-chains 145 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 988 GLN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8383 Z= 0.180 Angle : 0.548 8.120 11335 Z= 0.284 Chirality : 0.045 0.409 1244 Planarity : 0.003 0.031 1428 Dihedral : 5.857 57.221 1221 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.84 % Allowed : 14.79 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.80 (0.27), residues: 1006 helix: 2.01 (0.25), residues: 413 sheet: 0.31 (0.33), residues: 231 loop : -1.07 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 985 HIS 0.005 0.001 HIS A 387 PHE 0.018 0.001 PHE A 512 TYR 0.013 0.001 TYR B1111 ARG 0.007 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5954 (tpp80) cc_final: 0.5732 (mtp85) REVERT: A 146 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7708 (tm-30) REVERT: A 197 MET cc_start: 0.6241 (mtm) cc_final: 0.5737 (ttm) REVERT: A 227 ASP cc_start: 0.7953 (m-30) cc_final: 0.7572 (m-30) REVERT: A 301 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7673 (ttp) REVERT: A 366 LYS cc_start: 0.5970 (mtmt) cc_final: 0.5769 (mttm) REVERT: A 372 MET cc_start: 0.7254 (mtm) cc_final: 0.6973 (mmm) REVERT: A 444 ARG cc_start: 0.5868 (ttp-110) cc_final: 0.5393 (ttt180) REVERT: A 491 ARG cc_start: 0.7380 (tmt170) cc_final: 0.7019 (tpt-90) REVERT: A 520 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7398 (tpt170) REVERT: A 522 LYS cc_start: 0.7368 (ttpt) cc_final: 0.7165 (tppt) REVERT: A 563 GLU cc_start: 0.8207 (pt0) cc_final: 0.7379 (tp30) REVERT: A 567 VAL cc_start: 0.7659 (t) cc_final: 0.7417 (m) REVERT: A 619 MET cc_start: 0.7190 (mmt) cc_final: 0.6837 (tpt) REVERT: A 742 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6705 (tm-30) REVERT: B 910 ASP cc_start: 0.5191 (t0) cc_final: 0.4962 (t0) REVERT: B 947 ILE cc_start: 0.8066 (tt) cc_final: 0.7746 (tp) REVERT: B 1106 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6194 (mp10) REVERT: B 1209 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5239 (pp) REVERT: B 1219 GLN cc_start: 0.6860 (pt0) cc_final: 0.6591 (pt0) REVERT: B 1226 LYS cc_start: 0.6902 (pttm) cc_final: 0.6698 (ptmm) REVERT: B 1246 ASP cc_start: 0.6726 (p0) cc_final: 0.6475 (p0) outliers start: 25 outliers final: 13 residues processed: 150 average time/residue: 1.1855 time to fit residues: 189.0588 Evaluate side-chains 143 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8383 Z= 0.238 Angle : 0.569 9.191 11335 Z= 0.296 Chirality : 0.045 0.359 1244 Planarity : 0.003 0.043 1428 Dihedral : 5.862 59.748 1221 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 15.70 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.74 (0.26), residues: 1006 helix: 1.97 (0.25), residues: 411 sheet: 0.33 (0.34), residues: 227 loop : -1.12 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 985 HIS 0.005 0.001 HIS A 494 PHE 0.011 0.001 PHE A 299 TYR 0.022 0.001 TYR B1133 ARG 0.008 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6004 (tpp80) cc_final: 0.5693 (mtp85) REVERT: A 146 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7678 (tm-30) REVERT: A 197 MET cc_start: 0.6212 (mtm) cc_final: 0.5026 (tpt) REVERT: A 301 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7692 (ttp) REVERT: A 366 LYS cc_start: 0.6015 (mtmt) cc_final: 0.5815 (mttm) REVERT: A 372 MET cc_start: 0.7214 (mtm) cc_final: 0.6957 (mmp) REVERT: A 444 ARG cc_start: 0.5967 (ttp-110) cc_final: 0.5599 (ttt180) REVERT: A 449 MET cc_start: 0.7142 (mtp) cc_final: 0.6908 (mtp) REVERT: A 491 ARG cc_start: 0.7381 (tmt170) cc_final: 0.6731 (tpt-90) REVERT: A 493 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: A 520 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7386 (tpt170) REVERT: A 563 GLU cc_start: 0.8217 (pt0) cc_final: 0.7455 (tp30) REVERT: A 567 VAL cc_start: 0.7688 (t) cc_final: 0.7433 (m) REVERT: A 619 MET cc_start: 0.7212 (mmt) cc_final: 0.6891 (tpt) REVERT: A 742 GLN cc_start: 0.6934 (tm-30) cc_final: 0.6632 (tm-30) REVERT: B 1061 ARG cc_start: 0.6336 (mtm-85) cc_final: 0.6030 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6093 (mp10) REVERT: B 1133 TYR cc_start: 0.5078 (p90) cc_final: 0.4596 (p90) REVERT: B 1193 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5802 (mm) REVERT: B 1209 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5243 (pp) outliers start: 26 outliers final: 13 residues processed: 141 average time/residue: 1.3020 time to fit residues: 194.0832 Evaluate side-chains 140 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.0060 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8383 Z= 0.182 Angle : 0.542 10.625 11335 Z= 0.281 Chirality : 0.043 0.321 1244 Planarity : 0.003 0.052 1428 Dihedral : 5.704 58.566 1221 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 16.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.79 (0.27), residues: 1006 helix: 1.98 (0.25), residues: 416 sheet: 0.36 (0.34), residues: 227 loop : -1.10 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.019 0.001 PHE A 512 TYR 0.013 0.001 TYR B1133 ARG 0.016 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5957 (tpp80) cc_final: 0.5616 (mtp85) REVERT: A 146 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7700 (tm-30) REVERT: A 197 MET cc_start: 0.6200 (mtm) cc_final: 0.4995 (tpt) REVERT: A 301 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (ttp) REVERT: A 372 MET cc_start: 0.7303 (mtm) cc_final: 0.7053 (mmp) REVERT: A 444 ARG cc_start: 0.5721 (ttp-110) cc_final: 0.5358 (ttt180) REVERT: A 491 ARG cc_start: 0.7328 (tmt170) cc_final: 0.6884 (tpt-90) REVERT: A 520 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7375 (tpt170) REVERT: A 563 GLU cc_start: 0.8210 (pt0) cc_final: 0.7424 (tp30) REVERT: A 567 VAL cc_start: 0.7680 (t) cc_final: 0.7432 (m) REVERT: A 619 MET cc_start: 0.7206 (mmt) cc_final: 0.6849 (tpt) REVERT: A 742 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6543 (tm-30) REVERT: B 910 ASP cc_start: 0.5305 (t0) cc_final: 0.5017 (t0) REVERT: B 1061 ARG cc_start: 0.6376 (mtm-85) cc_final: 0.6057 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.6102 (mp10) REVERT: B 1108 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7026 (t70) REVERT: B 1209 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5346 (pp) REVERT: B 1219 GLN cc_start: 0.6811 (pt0) cc_final: 0.5971 (pp30) REVERT: B 1246 ASP cc_start: 0.6778 (p0) cc_final: 0.6448 (p0) outliers start: 21 outliers final: 10 residues processed: 136 average time/residue: 1.3963 time to fit residues: 202.0959 Evaluate side-chains 137 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 0.0040 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.163 Angle : 0.542 11.447 11335 Z= 0.278 Chirality : 0.043 0.286 1244 Planarity : 0.003 0.049 1428 Dihedral : 5.500 59.507 1221 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 16.61 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.27), residues: 1006 helix: 2.18 (0.25), residues: 415 sheet: 0.47 (0.34), residues: 222 loop : -1.08 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.008 0.001 PHE A 459 TYR 0.018 0.001 TYR B1133 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5941 (tpp80) cc_final: 0.5586 (mtp85) REVERT: A 146 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7715 (tm-30) REVERT: A 197 MET cc_start: 0.6070 (mtm) cc_final: 0.4887 (tpt) REVERT: A 227 ASP cc_start: 0.7856 (m-30) cc_final: 0.7238 (m-30) REVERT: A 301 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7634 (ttp) REVERT: A 372 MET cc_start: 0.7282 (mtm) cc_final: 0.7037 (mmp) REVERT: A 444 ARG cc_start: 0.5724 (ttp-110) cc_final: 0.5283 (ttt180) REVERT: A 491 ARG cc_start: 0.7316 (tmt170) cc_final: 0.6606 (tpt-90) REVERT: A 493 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: A 520 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7381 (tpt170) REVERT: A 563 GLU cc_start: 0.8212 (pt0) cc_final: 0.7422 (tp30) REVERT: A 567 VAL cc_start: 0.7680 (t) cc_final: 0.7445 (m) REVERT: A 619 MET cc_start: 0.7115 (mmt) cc_final: 0.6832 (tpt) REVERT: A 742 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6551 (tm-30) REVERT: B 910 ASP cc_start: 0.5214 (t0) cc_final: 0.4991 (t0) REVERT: B 1061 ARG cc_start: 0.6400 (mtm-85) cc_final: 0.6082 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6124 (mp10) REVERT: B 1108 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6942 (t70) REVERT: B 1175 ARG cc_start: 0.5650 (mtm-85) cc_final: 0.5267 (mtm-85) REVERT: B 1193 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5808 (mm) REVERT: B 1246 ASP cc_start: 0.6769 (p0) cc_final: 0.6427 (p0) outliers start: 28 outliers final: 12 residues processed: 148 average time/residue: 1.1807 time to fit residues: 185.8141 Evaluate side-chains 139 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8383 Z= 0.298 Angle : 0.611 13.033 11335 Z= 0.315 Chirality : 0.045 0.334 1244 Planarity : 0.003 0.039 1428 Dihedral : 5.447 58.972 1221 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.96 % Allowed : 16.72 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.66 (0.26), residues: 1006 helix: 1.83 (0.25), residues: 412 sheet: 0.24 (0.34), residues: 229 loop : -1.05 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1014 HIS 0.004 0.001 HIS A 378 PHE 0.018 0.002 PHE A 512 TYR 0.019 0.002 TYR A 306 ARG 0.014 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6061 (tpp80) cc_final: 0.5570 (mtp85) REVERT: A 146 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7665 (tm-30) REVERT: A 197 MET cc_start: 0.6015 (mtm) cc_final: 0.4859 (tmm) REVERT: A 227 ASP cc_start: 0.7907 (m-30) cc_final: 0.7670 (m-30) REVERT: A 301 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7711 (ttp) REVERT: A 372 MET cc_start: 0.7246 (mtm) cc_final: 0.6982 (mmp) REVERT: A 444 ARG cc_start: 0.6001 (ttp-110) cc_final: 0.5649 (ttt180) REVERT: A 491 ARG cc_start: 0.7360 (tmt170) cc_final: 0.6635 (tpt-90) REVERT: A 493 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: A 520 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7421 (tpt170) REVERT: A 563 GLU cc_start: 0.8250 (pt0) cc_final: 0.7518 (tp30) REVERT: A 567 VAL cc_start: 0.7748 (t) cc_final: 0.7484 (m) REVERT: A 619 MET cc_start: 0.7176 (mmt) cc_final: 0.6884 (tpt) REVERT: A 742 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 1061 ARG cc_start: 0.6390 (mtm-85) cc_final: 0.6049 (ptp-170) REVERT: B 1108 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6976 (t70) REVERT: B 1219 GLN cc_start: 0.6956 (pt0) cc_final: 0.6068 (pp30) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 1.2535 time to fit residues: 190.3658 Evaluate side-chains 140 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.0010 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8383 Z= 0.248 Angle : 0.592 13.474 11335 Z= 0.304 Chirality : 0.044 0.320 1244 Planarity : 0.003 0.054 1428 Dihedral : 5.185 59.355 1221 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer: Outliers : 2.62 % Allowed : 17.06 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.66 (0.26), residues: 1006 helix: 1.87 (0.25), residues: 411 sheet: 0.24 (0.34), residues: 224 loop : -1.07 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 985 HIS 0.005 0.001 HIS A 494 PHE 0.009 0.001 PHE A 499 TYR 0.017 0.001 TYR A 306 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6087 (tpp80) cc_final: 0.5604 (mtp85) REVERT: A 146 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7671 (tm-30) REVERT: A 197 MET cc_start: 0.6001 (mtm) cc_final: 0.4843 (tmm) REVERT: A 227 ASP cc_start: 0.7938 (m-30) cc_final: 0.7720 (m-30) REVERT: A 252 VAL cc_start: 0.5865 (OUTLIER) cc_final: 0.5654 (p) REVERT: A 301 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7695 (ttp) REVERT: A 372 MET cc_start: 0.7277 (mtm) cc_final: 0.7001 (mmp) REVERT: A 382 MET cc_start: 0.6042 (mmt) cc_final: 0.5775 (mpt) REVERT: A 444 ARG cc_start: 0.5985 (ttp-110) cc_final: 0.5636 (ttt180) REVERT: A 491 ARG cc_start: 0.7341 (tmt170) cc_final: 0.6615 (tpt-90) REVERT: A 493 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7431 (tpt170) REVERT: A 563 GLU cc_start: 0.8244 (pt0) cc_final: 0.7503 (tp30) REVERT: A 567 VAL cc_start: 0.7787 (t) cc_final: 0.7526 (m) REVERT: A 619 MET cc_start: 0.7278 (mmt) cc_final: 0.6904 (tpt) REVERT: A 742 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 910 ASP cc_start: 0.5236 (t0) cc_final: 0.5034 (t0) REVERT: B 1061 ARG cc_start: 0.6384 (mtm-85) cc_final: 0.6035 (ptp-170) REVERT: B 1108 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 1219 GLN cc_start: 0.6983 (pt0) cc_final: 0.6057 (pp30) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 1.1540 time to fit residues: 167.0989 Evaluate side-chains 143 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6986 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8383 Z= 0.192 Angle : 0.574 14.224 11335 Z= 0.294 Chirality : 0.043 0.300 1244 Planarity : 0.003 0.055 1428 Dihedral : 4.982 59.412 1221 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 17.29 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1006 helix: 2.08 (0.25), residues: 411 sheet: 0.31 (0.34), residues: 229 loop : -1.02 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.019 0.001 PHE A 512 TYR 0.015 0.001 TYR B1133 ARG 0.016 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6096 (tpp80) cc_final: 0.5608 (mtp85) REVERT: A 146 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7690 (tm-30) REVERT: A 197 MET cc_start: 0.5917 (mtm) cc_final: 0.4760 (tmm) REVERT: A 298 MET cc_start: 0.8068 (mmt) cc_final: 0.7661 (mmt) REVERT: A 301 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: A 372 MET cc_start: 0.7267 (mtm) cc_final: 0.6989 (mmp) REVERT: A 382 MET cc_start: 0.6043 (mmt) cc_final: 0.5807 (mpt) REVERT: A 444 ARG cc_start: 0.5932 (ttp-110) cc_final: 0.5591 (ttt180) REVERT: A 491 ARG cc_start: 0.7369 (tmt170) cc_final: 0.6648 (tpt-90) REVERT: A 493 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7434 (tpt170) REVERT: A 563 GLU cc_start: 0.8230 (pt0) cc_final: 0.7535 (tp30) REVERT: A 567 VAL cc_start: 0.7786 (t) cc_final: 0.7528 (m) REVERT: A 742 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 1021 ASN cc_start: 0.6507 (m-40) cc_final: 0.6290 (m110) REVERT: B 1061 ARG cc_start: 0.6376 (mtm-85) cc_final: 0.6030 (ptp-170) REVERT: B 1108 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6948 (t0) REVERT: B 1209 LEU cc_start: 0.6329 (mm) cc_final: 0.5819 (pp) REVERT: B 1219 GLN cc_start: 0.7004 (pt0) cc_final: 0.6142 (pp30) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 1.2779 time to fit residues: 180.2003 Evaluate side-chains 136 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.220946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143473 restraints weight = 8872.344| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.53 r_work: 0.3504 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.174 Angle : 0.551 11.660 11335 Z= 0.288 Chirality : 0.043 0.287 1244 Planarity : 0.003 0.029 1428 Dihedral : 4.844 59.866 1221 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.39 % Allowed : 17.97 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.97 (0.27), residues: 1006 helix: 2.18 (0.25), residues: 411 sheet: 0.38 (0.35), residues: 229 loop : -0.97 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.008 0.001 PHE A 459 TYR 0.015 0.001 TYR B1133 ARG 0.007 0.000 ARG B 903 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.88 seconds wall clock time: 68 minutes 11.09 seconds (4091.09 seconds total)