Starting phenix.real_space_refine (version: dev) on Mon Apr 4 16:20:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6y_31753/04_2022/7v6y_31753_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7326 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 44, 'TRANS': 945} Chain breaks: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 29, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Unusual residues: {'5VI': 1, 'NAG': 3, 'CLR': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.87, per 1000 atoms: 0.65 Number of scatterers: 7484 At special positions: 0 Unit cell: (93.48, 86.92, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1301 8.00 N 1221 7.00 C 4923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1204 " - " ASN A 127 " " NAG A1206 " - " ASN A 400 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 3 sheets defined 57.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.662A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 217 through 220 removed outlier: 3.572A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.786A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 396 removed outlier: 4.529A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 456 through 477 removed outlier: 3.768A pdb=" N LEU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 513 Proline residue: A 490 - end of helix removed outlier: 4.007A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 548 removed outlier: 4.932A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 574 Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.799A pdb=" N ILE A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 733 through 755 removed outlier: 4.066A pdb=" N VAL A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 803 through 814 removed outlier: 3.931A pdb=" N HIS A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 810 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 851 Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.573A pdb=" N LEU A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.512A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU A1005 " --> pdb=" O PHE A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1000 through 1005' Processing helix chain 'A' and resid 1010 through 1033 Processing helix chain 'A' and resid 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1092 removed outlier: 4.566A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1128 removed outlier: 3.747A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 4.557A pdb=" N GLY A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1163 removed outlier: 3.804A pdb=" N PHE A1139 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 345 through 352 Processing sheet with id= B, first strand: chain 'A' and resid 786 through 788 Processing sheet with id= C, first strand: chain 'A' and resid 789 through 793 404 hydrogen bonds defined for protein. 1206 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: 2.10 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1135 1.28 - 1.41: 2003 1.41 - 1.54: 4444 1.54 - 1.68: 32 1.68 - 1.81: 60 Bond restraints: 7674 Sorted by residual: bond pdb=" C LEU A1145 " pdb=" O LEU A1145 " ideal model delta sigma weight residual 1.237 1.146 0.090 1.17e-02 7.31e+03 5.98e+01 bond pdb=" CA HIS A 164 " pdb=" C HIS A 164 " ideal model delta sigma weight residual 1.523 1.425 0.099 1.30e-02 5.92e+03 5.77e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.92e+01 bond pdb=" CA GLN A 228 " pdb=" C GLN A 228 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.24e-02 6.50e+03 4.92e+01 bond pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.31e+01 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.67: 269 105.67 - 113.45: 4059 113.45 - 121.24: 4682 121.24 - 129.03: 1426 129.03 - 136.82: 76 Bond angle restraints: 10512 Sorted by residual: angle pdb=" N THR A 293 " pdb=" CA THR A 293 " pdb=" C THR A 293 " ideal model delta sigma weight residual 113.17 99.29 13.88 1.26e+00 6.30e-01 1.21e+02 angle pdb=" N LYS A 339 " pdb=" CA LYS A 339 " pdb=" C LYS A 339 " ideal model delta sigma weight residual 111.28 122.74 -11.46 1.09e+00 8.42e-01 1.10e+02 angle pdb=" N GLN A 794 " pdb=" CA GLN A 794 " pdb=" C GLN A 794 " ideal model delta sigma weight residual 111.14 122.39 -11.25 1.08e+00 8.57e-01 1.09e+02 angle pdb=" N THR A 764 " pdb=" CA THR A 764 " pdb=" C THR A 764 " ideal model delta sigma weight residual 113.23 101.13 12.10 1.24e+00 6.50e-01 9.53e+01 angle pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" C3 NAG B 1 " ideal model delta sigma weight residual 110.19 101.60 8.59 9.25e-01 1.17e+00 8.62e+01 ... (remaining 10507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3924 16.95 - 33.90: 343 33.90 - 50.86: 123 50.86 - 67.81: 40 67.81 - 84.76: 5 Dihedral angle restraints: 4435 sinusoidal: 1548 harmonic: 2887 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual 93.00 171.16 -78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" C PHE A1131 " pdb=" N PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual -122.60 -138.95 16.35 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual 122.80 138.50 -15.70 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 4432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 977 0.139 - 0.278: 234 0.278 - 0.418: 39 0.418 - 0.557: 11 0.557 - 0.696: 4 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA PHE A 743 " pdb=" N PHE A 743 " pdb=" C PHE A 743 " pdb=" CB PHE A 743 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE A1131 " pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CB PHE A1131 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP A 183 " pdb=" N TRP A 183 " pdb=" C TRP A 183 " pdb=" CB TRP A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.50e+00 ... (remaining 1262 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.199 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" C7 NAG B 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.086 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A1158 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 361 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C HIS A 361 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS A 361 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE A 362 " 0.030 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2192 2.79 - 3.31: 7534 3.31 - 3.84: 12243 3.84 - 4.37: 14514 4.37 - 4.90: 23414 Nonbonded interactions: 59897 Sorted by model distance: nonbonded pdb=" OE2 GLU A 108 " pdb=" CB SER A 480 " model vdw 2.258 3.440 nonbonded pdb=" O SER A 401 " pdb=" OG1 THR A 402 " model vdw 2.269 2.440 nonbonded pdb=" N THR A 293 " pdb=" N ALA A 294 " model vdw 2.281 2.560 nonbonded pdb=" O PHE A 545 " pdb=" OG SER A 560 " model vdw 2.339 2.440 nonbonded pdb=" N MET A 178 " pdb=" O MET A 178 " model vdw 2.342 2.496 ... (remaining 59892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 4923 2.51 5 N 1221 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.510 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 24.020 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.014 0.099 7674 Z= 0.923 Angle : 1.828 13.878 10512 Z= 1.266 Chirality : 0.132 0.696 1265 Planarity : 0.012 0.164 1295 Dihedral : 15.847 84.758 2566 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.51 % Rotamer Outliers : 11.06 % Cbeta Deviations : 0.97 % 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: 0.59 (0.26), residues: 984 helix: 1.40 (0.21), residues: 589 sheet: 0.32 (0.72), residues: 49 loop : -1.38 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 172 time to evaluate : 0.920 Fit side-chains outliers start: 78 outliers final: 20 residues processed: 226 average time/residue: 0.1836 time to fit residues: 56.4029 Evaluate side-chains 145 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0752 time to fit residues: 3.8861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 269 ASN A 284 ASN A 322 HIS A 351 GLN A 452 GLN A 506 HIS A 570 ASN A 780 GLN A 800 ASN A 809 HIS A 891 GLN A 901 ASN A 985 ASN A1085 HIS ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 7674 Z= 0.238 Angle : 0.694 7.535 10512 Z= 0.366 Chirality : 0.044 0.206 1265 Planarity : 0.007 0.073 1295 Dihedral : 7.641 79.417 1116 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 984 helix: 1.37 (0.21), residues: 594 sheet: 0.41 (0.75), residues: 48 loop : -1.48 (0.31), residues: 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.863 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 155 average time/residue: 0.1751 time to fit residues: 38.1303 Evaluate side-chains 128 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1398 time to fit residues: 3.6766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 403 GLN A 452 GLN A 506 HIS A 794 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 7674 Z= 0.201 Angle : 0.601 7.170 10512 Z= 0.309 Chirality : 0.041 0.195 1265 Planarity : 0.006 0.050 1295 Dihedral : 6.794 67.183 1116 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 2.70 % 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: 0.77 (0.26), residues: 984 helix: 1.54 (0.21), residues: 595 sheet: 0.35 (0.74), residues: 48 loop : -1.32 (0.32), residues: 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 0.752 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.1745 time to fit residues: 37.9458 Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0736 time to fit residues: 2.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.0040 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7674 Z= 0.211 Angle : 0.586 7.426 10512 Z= 0.296 Chirality : 0.040 0.188 1265 Planarity : 0.005 0.052 1295 Dihedral : 6.620 56.818 1116 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 2.27 % 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: 0.81 (0.26), residues: 984 helix: 1.58 (0.21), residues: 595 sheet: 0.33 (0.76), residues: 48 loop : -1.32 (0.32), residues: 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.1855 time to fit residues: 34.0045 Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0868 time to fit residues: 2.9502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 7674 Z= 0.300 Angle : 0.624 8.709 10512 Z= 0.317 Chirality : 0.042 0.172 1265 Planarity : 0.006 0.075 1295 Dihedral : 6.497 52.729 1116 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 984 helix: 1.29 (0.21), residues: 598 sheet: 0.02 (0.79), residues: 48 loop : -1.40 (0.31), residues: 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.810 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 133 average time/residue: 0.1683 time to fit residues: 32.3005 Evaluate side-chains 118 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0747 time to fit residues: 1.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 269 ASN A 344 HIS ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.190 Angle : 0.572 9.198 10512 Z= 0.287 Chirality : 0.039 0.172 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.281 56.946 1116 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 984 helix: 1.53 (0.21), residues: 591 sheet: 0.90 (0.94), residues: 37 loop : -1.46 (0.30), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.809 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1769 time to fit residues: 29.8667 Evaluate side-chains 116 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0987 time to fit residues: 1.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 40.0000 chunk 95 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 794 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7674 Z= 0.246 Angle : 0.602 10.910 10512 Z= 0.300 Chirality : 0.041 0.170 1265 Planarity : 0.005 0.058 1295 Dihedral : 6.147 57.320 1116 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.26), residues: 984 helix: 1.47 (0.21), residues: 590 sheet: -0.15 (0.83), residues: 48 loop : -1.41 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.1731 time to fit residues: 31.4806 Evaluate side-chains 117 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0742 time to fit residues: 1.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.192 Angle : 0.584 10.040 10512 Z= 0.294 Chirality : 0.040 0.191 1265 Planarity : 0.006 0.106 1295 Dihedral : 5.952 52.590 1116 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.27), residues: 984 helix: 1.66 (0.21), residues: 585 sheet: 0.65 (0.96), residues: 37 loop : -1.54 (0.31), residues: 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.792 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 119 average time/residue: 0.1670 time to fit residues: 28.2222 Evaluate side-chains 111 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0794 time to fit residues: 1.2506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.0270 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7674 Z= 0.273 Angle : 0.638 9.536 10512 Z= 0.323 Chirality : 0.042 0.169 1265 Planarity : 0.006 0.093 1295 Dihedral : 6.011 53.305 1116 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.57 (0.27), residues: 984 helix: 1.49 (0.21), residues: 594 sheet: 0.60 (0.94), residues: 37 loop : -1.64 (0.31), residues: 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 120 average time/residue: 0.1766 time to fit residues: 30.3198 Evaluate side-chains 116 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0844 time to fit residues: 1.4357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.197 Angle : 0.606 9.828 10512 Z= 0.305 Chirality : 0.040 0.170 1265 Planarity : 0.006 0.085 1295 Dihedral : 5.838 51.214 1116 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 984 helix: 1.63 (0.21), residues: 591 sheet: 1.02 (1.01), residues: 33 loop : -1.66 (0.31), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.1791 time to fit residues: 29.0299 Evaluate side-chains 113 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0863 time to fit residues: 1.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 832 HIS ** 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 = 0.4660 r_free = 0.4660 target = 0.245414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.202251 restraints weight = 7938.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.201914 restraints weight = 9689.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202938 restraints weight = 6152.788| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7674 Z= 0.195 Angle : 0.596 9.839 10512 Z= 0.297 Chirality : 0.040 0.169 1265 Planarity : 0.006 0.077 1295 Dihedral : 5.695 52.136 1116 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.43 % 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: 0.79 (0.27), residues: 984 helix: 1.73 (0.21), residues: 585 sheet: 1.03 (1.01), residues: 33 loop : -1.61 (0.31), residues: 366 =============================================================================== Job complete usr+sys time: 1598.76 seconds wall clock time: 29 minutes 46.54 seconds (1786.54 seconds total)