Starting phenix.real_space_refine on Mon Nov 13 21:56:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvh_12604/11_2023/7nvh_12604_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.067 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 27 5.16 5 C 3605 2.51 5 N 913 2.21 5 O 983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 692": "OD1" <-> "OD2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 715": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 5528 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5528 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 718, 5509 Unusual residues: {'AV0': 1} Classifications: {'peptide': 717, 'undetermined': 1} Link IDs: {'PTRANS': 35, 'TRANS': 681, None: 1} Not linked: pdbres="PRO A 752 " pdbres="AV0 A 801 " Chain breaks: 1 Conformer: "B" Number of residues, atoms: 718, 5509 Unusual residues: {'AV0': 1} Classifications: {'peptide': 717, 'undetermined': 1} Link IDs: {'PTRANS': 35, 'TRANS': 681, None: 1} Not linked: pdbres="PRO A 752 " pdbres="AV0 A 801 " Chain breaks: 1 bond proxies already assigned to first conformer: 5604 Time building chain proxies: 6.03, per 1000 atoms: 1.09 Number of scatterers: 5528 At special positions: 0 Unit cell: (82.368, 72.384, 106.496, 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 27 16.00 O 983 8.00 N 913 7.00 C 3605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 2 sheets defined 63.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.100A pdb=" N ARG A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 25 No H-bonds generated for 'chain 'A' and resid 22 through 25' Processing helix chain 'A' and resid 31 through 37 removed outlier: 4.417A pdb=" N GLY A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.510A pdb=" N ILE A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 166 through 200 removed outlier: 4.704A pdb=" N ILE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 203 through 229 Proline residue: A 209 - end of helix removed outlier: 3.598A pdb=" N ILE A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.609A pdb=" N GLN A 238 " --> pdb=" O TYR A 235 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.707A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 301 removed outlier: 4.167A pdb=" N ARG A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 removed outlier: 3.667A pdb=" N TYR A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Proline residue: A 330 - end of helix removed outlier: 6.785A pdb=" N LYS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.669A pdb=" N VAL A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 391' Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.869A pdb=" N ALA A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.325A pdb=" N SER A 522 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 525 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 526 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.510A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.876A pdb=" N VAL A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 606 Processing helix chain 'A' and resid 612 through 615 No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 624 through 655 removed outlier: 4.205A pdb=" N ARG A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 669 Processing helix chain 'A' and resid 671 through 689 removed outlier: 3.620A pdb=" N PHE A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 Processing helix chain 'A' and resid 714 through 726 removed outlier: 4.629A pdb=" N VAL A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 728 through 731 removed outlier: 3.735A pdb=" N TRP A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 731' Processing helix chain 'A' and resid 735 through 744 Processing sheet with id= A, first strand: chain 'A' and resid 127 through 131 Processing sheet with id= B, first strand: chain 'A' and resid 508 through 514 293 hydrogen bonds defined for protein. 826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 868 1.32 - 1.44: 1423 1.44 - 1.56: 3298 1.56 - 1.68: 11 1.68 - 1.81: 50 Bond restraints: 5650 Sorted by residual: bond pdb=" CCS AV0 A 801 " pdb=" OBZ AV0 A 801 " ideal model delta sigma weight residual 1.392 1.480 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 AV0 A 801 " pdb=" O5 AV0 A 801 " ideal model delta sigma weight residual 1.403 1.483 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CCR AV0 A 801 " pdb=" OBY AV0 A 801 " ideal model delta sigma weight residual 1.392 1.471 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" CBT AV0 A 801 " pdb=" CCM AV0 A 801 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CCJ AV0 A 801 " pdb=" OBX AV0 A 801 " ideal model delta sigma weight residual 1.403 1.474 -0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 5645 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 175 106.76 - 113.58: 3281 113.58 - 120.40: 2189 120.40 - 127.22: 1987 127.22 - 134.04: 61 Bond angle restraints: 7693 Sorted by residual: angle pdb=" N ASP A 640 " pdb=" CA ASP A 640 " pdb=" C ASP A 640 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N ASN A 390 " pdb=" CA ASN A 390 " pdb=" C ASN A 390 " ideal model delta sigma weight residual 114.75 110.33 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" C4 AV0 A 801 " pdb=" O4 AV0 A 801 " pdb=" CCR AV0 A 801 " ideal model delta sigma weight residual 119.55 110.89 8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" CA TYR A 698 " pdb=" CB TYR A 698 " pdb=" CG TYR A 698 " ideal model delta sigma weight residual 113.90 119.02 -5.12 1.80e+00 3.09e-01 8.09e+00 angle pdb=" C ASP A 710 " pdb=" CA ASP A 710 " pdb=" CB ASP A 710 " ideal model delta sigma weight residual 110.31 104.45 5.86 2.09e+00 2.29e-01 7.85e+00 ... (remaining 7688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 3105 22.47 - 44.93: 198 44.93 - 67.40: 20 67.40 - 89.87: 2 89.87 - 112.34: 1 Dihedral angle restraints: 3326 sinusoidal: 1281 harmonic: 2045 Sorted by residual: dihedral pdb=" CA LEU A 94 " pdb=" C LEU A 94 " pdb=" N ASN A 95 " pdb=" CA ASN A 95 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA VAL A 389 " pdb=" C VAL A 389 " pdb=" N ASN A 390 " pdb=" CA ASN A 390 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N PHE A 97 " pdb=" CA PHE A 97 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 650 0.044 - 0.088: 215 0.088 - 0.132: 53 0.132 - 0.176: 10 0.176 - 0.220: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CCS AV0 A 801 " pdb=" CCW AV0 A 801 " pdb=" OBZ AV0 A 801 " pdb=" OCB AV0 A 801 " both_signs ideal model delta sigma weight residual False 2.24 2.46 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CCQ AV0 A 801 " pdb=" CCF AV0 A 801 " pdb=" CCH AV0 A 801 " pdb=" OCB AV0 A 801 " both_signs ideal model delta sigma weight residual False 2.54 2.34 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN A 238 " pdb=" N GLN A 238 " pdb=" C GLN A 238 " pdb=" CB GLN A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 927 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 83 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 84 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 75 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 76 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 583 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 584 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.027 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 106 2.70 - 3.25: 5597 3.25 - 3.80: 8837 3.80 - 4.35: 11746 4.35 - 4.90: 19795 Nonbonded interactions: 46081 Sorted by model distance: nonbonded pdb=" O ILE A 323 " pdb=" OG1 THR A 327 " model vdw 2.145 2.440 nonbonded pdb=" OG1 THR A 659 " pdb=" OD1 ASP A 728 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR A 61 " pdb=" OE2 GLU A 495 " model vdw 2.252 2.440 nonbonded pdb=" O SER A 66 " pdb=" OG SER A 131 " model vdw 2.298 2.440 nonbonded pdb=" NH2 ARG A 65 " pdb=" O GLY A 136 " model vdw 2.327 2.520 ... (remaining 46076 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=0.50 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.990 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.080 Find NCS groups from input model: 0.180 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.006 0.088 5650 Z= 0.396 Angle : 0.726 9.163 7693 Z= 0.374 Chirality : 0.046 0.220 930 Planarity : 0.005 0.054 950 Dihedral : 14.268 112.335 2018 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.69 % Allowed : 0.17 % Favored : 99.13 % 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: -0.42 (0.33), residues: 716 helix: 0.17 (0.25), residues: 479 sheet: -0.78 (0.86), residues: 38 loop : -0.98 (0.46), residues: 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.583 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.9705 time to fit residues: 67.8906 Evaluate side-chains 58 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5650 Z= 0.198 Angle : 0.587 8.745 7693 Z= 0.295 Chirality : 0.041 0.161 930 Planarity : 0.005 0.050 950 Dihedral : 7.766 119.655 791 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.56 % Allowed : 5.02 % Favored : 93.43 % 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: -0.10 (0.33), residues: 716 helix: 0.43 (0.25), residues: 481 sheet: -0.53 (0.87), residues: 38 loop : -0.95 (0.47), residues: 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.620 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 1.0873 time to fit residues: 71.1566 Evaluate side-chains 62 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8084 time to fit residues: 4.1798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5650 Z= 0.253 Angle : 0.590 8.095 7693 Z= 0.294 Chirality : 0.042 0.169 930 Planarity : 0.005 0.046 950 Dihedral : 7.762 120.500 791 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.25 % Allowed : 6.57 % Favored : 91.18 % 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: 0.15 (0.33), residues: 716 helix: 0.64 (0.26), residues: 474 sheet: -0.34 (0.87), residues: 38 loop : -0.91 (0.45), residues: 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.630 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 1.0972 time to fit residues: 74.2031 Evaluate side-chains 64 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.6096 time to fit residues: 4.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5650 Z= 0.224 Angle : 0.570 8.737 7693 Z= 0.283 Chirality : 0.041 0.163 930 Planarity : 0.005 0.045 950 Dihedral : 7.656 120.924 791 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.42 % Allowed : 7.79 % Favored : 89.79 % 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: 0.27 (0.33), residues: 716 helix: 0.74 (0.26), residues: 473 sheet: -0.37 (0.87), residues: 38 loop : -0.84 (0.45), residues: 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.580 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 1.1092 time to fit residues: 76.0474 Evaluate side-chains 64 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 1.2154 time to fit residues: 4.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5650 Z= 0.238 Angle : 0.575 8.976 7693 Z= 0.285 Chirality : 0.042 0.161 930 Planarity : 0.005 0.045 950 Dihedral : 7.595 120.916 791 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.08 % Allowed : 9.52 % Favored : 88.41 % 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: 0.31 (0.33), residues: 716 helix: 0.78 (0.26), residues: 473 sheet: -0.46 (0.86), residues: 38 loop : -0.83 (0.45), residues: 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.660 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 1.1631 time to fit residues: 76.0214 Evaluate side-chains 65 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.8483 time to fit residues: 5.2659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.3980 chunk 68 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 overall best weight: 0.2710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5650 Z= 0.142 Angle : 0.531 9.951 7693 Z= 0.258 Chirality : 0.039 0.152 930 Planarity : 0.004 0.044 950 Dihedral : 7.391 120.756 791 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.73 % Allowed : 10.21 % Favored : 88.06 % 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: 0.60 (0.33), residues: 716 helix: 1.02 (0.26), residues: 469 sheet: -0.67 (0.82), residues: 39 loop : -0.65 (0.45), residues: 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.617 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 1.0863 time to fit residues: 80.3473 Evaluate side-chains 60 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.4957 time to fit residues: 2.4076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5650 Z= 0.246 Angle : 0.579 9.910 7693 Z= 0.286 Chirality : 0.042 0.159 930 Planarity : 0.005 0.045 950 Dihedral : 7.398 120.790 791 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.56 % Allowed : 10.55 % Favored : 87.89 % 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: 0.57 (0.33), residues: 716 helix: 0.96 (0.26), residues: 470 sheet: -0.40 (0.85), residues: 38 loop : -0.66 (0.45), residues: 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.617 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.1995 time to fit residues: 75.7068 Evaluate side-chains 61 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 3 average time/residue: 0.1294 time to fit residues: 1.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5650 Z= 0.242 Angle : 0.569 10.179 7693 Z= 0.281 Chirality : 0.042 0.162 930 Planarity : 0.005 0.044 950 Dihedral : 7.365 121.196 791 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.21 % Allowed : 11.42 % Favored : 87.37 % 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: 0.47 (0.33), residues: 716 helix: 0.92 (0.26), residues: 470 sheet: -0.77 (0.82), residues: 40 loop : -0.70 (0.45), residues: 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.635 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 1.0707 time to fit residues: 67.8242 Evaluate side-chains 62 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 0.6563 time to fit residues: 3.5591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5650 Z= 0.239 Angle : 0.573 11.038 7693 Z= 0.283 Chirality : 0.042 0.159 930 Planarity : 0.005 0.054 950 Dihedral : 7.339 121.266 791 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.87 % Allowed : 11.76 % Favored : 87.37 % 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: 0.52 (0.33), residues: 716 helix: 0.91 (0.25), residues: 471 sheet: -0.72 (0.75), residues: 46 loop : -0.56 (0.47), residues: 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.554 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 1.0929 time to fit residues: 69.8462 Evaluate side-chains 59 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1075 time to fit residues: 0.9817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.0270 chunk 44 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 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 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5650 Z= 0.184 Angle : 0.558 10.722 7693 Z= 0.272 Chirality : 0.041 0.154 930 Planarity : 0.005 0.044 950 Dihedral : 7.243 120.994 791 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.69 % Allowed : 12.28 % Favored : 87.02 % 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: 0.58 (0.33), residues: 716 helix: 1.00 (0.26), residues: 469 sheet: -0.83 (0.80), residues: 41 loop : -0.61 (0.46), residues: 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.588 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 1.1530 time to fit residues: 74.2571 Evaluate side-chains 59 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1161 time to fit residues: 1.1720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 45 optimal weight: 0.0670 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112105 restraints weight = 20577.001| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.05 r_work: 0.3164 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5650 Z= 0.142 Angle : 0.537 11.578 7693 Z= 0.262 Chirality : 0.040 0.169 930 Planarity : 0.005 0.057 950 Dihedral : 7.107 120.382 791 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 12.28 % Favored : 87.02 % 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 (0.33), residues: 716 helix: 1.12 (0.26), residues: 471 sheet: -0.58 (0.82), residues: 39 loop : -0.43 (0.46), residues: 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.08 seconds wall clock time: 38 minutes 0.94 seconds (2280.94 seconds total)