Starting phenix.real_space_refine on Sat Dec 9 05:10:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/12_2023/6ny3_8980.pdb" } resolution = 3.7 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= 0.004 sd= 0.110 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 164 5.49 5 S 21 5.16 5 C 5880 2.51 5 N 1863 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 51": "OE1" <-> "OE2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y ASP 90": "OD1" <-> "OD2" Residue "Y PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 249": "OE1" <-> "OE2" Residue "Y GLU 266": "OE1" <-> "OE2" Residue "Y GLU 288": "OE1" <-> "OE2" Residue "Y TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 388": "OD1" <-> "OD2" Residue "Y TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 474": "OE1" <-> "OE2" Residue "Y ARG 475": "NH1" <-> "NH2" Residue "Y TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 488": "OE1" <-> "OE2" Residue "Y ASP 513": "OD1" <-> "OD2" Residue "Y PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 794": "OD1" <-> "OD2" Residue "Y TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 955": "OE1" <-> "OE2" Residue "Y TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10214 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 485 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Y" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6771 Classifications: {'peptide': 915} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 193} Link IDs: {'PTRANS': 29, 'TRANS': 885} Chain breaks: 8 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 121, 'ASP:plan': 16, 'GLU:plan': 26, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2344 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45} Link IDs: {'rna2p': 10, 'rna3p': 99} Chain breaks: 2 Time building chain proxies: 6.35, per 1000 atoms: 0.62 Number of scatterers: 10214 At special positions: 0 Unit cell: (97.2, 139.5, 123.3, 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 21 16.00 P 164 15.00 O 2286 8.00 N 1863 7.00 C 5880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Y 826 " - pdb=" SG CYS Y 928 " distance=2.02 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: 4.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 44.5% alpha, 7.7% beta 63 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 13 removed outlier: 3.566A pdb=" N ILE Y 8 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 9 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS Y 10 " --> pdb=" O ASN Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 60 through 88 removed outlier: 3.641A pdb=" N ASN Y 64 " --> pdb=" O ASN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 222 through 260 removed outlier: 4.440A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 271 removed outlier: 4.476A pdb=" N ALA Y 268 " --> pdb=" O LEU Y 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 308 Processing helix chain 'Y' and resid 343 through 357 removed outlier: 3.953A pdb=" N LYS Y 357 " --> pdb=" O LEU Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 366 removed outlier: 3.917A pdb=" N TRP Y 365 " --> pdb=" O GLY Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 371 through 380 Processing helix chain 'Y' and resid 404 through 417 Processing helix chain 'Y' and resid 423 through 429 removed outlier: 4.306A pdb=" N ASP Y 427 " --> pdb=" O GLY Y 423 " (cutoff:3.500A) Processing helix chain 'Y' and resid 433 through 448 removed outlier: 3.575A pdb=" N LEU Y 440 " --> pdb=" O LYS Y 436 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS Y 443 " --> pdb=" O GLY Y 439 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Y 445 " --> pdb=" O THR Y 441 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG Y 446 " --> pdb=" O SER Y 442 " (cutoff:3.500A) Processing helix chain 'Y' and resid 458 through 473 Processing helix chain 'Y' and resid 475 through 480 Processing helix chain 'Y' and resid 481 through 501 removed outlier: 4.371A pdb=" N TYR Y 485 " --> pdb=" O GLU Y 481 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA Y 486 " --> pdb=" O LYS Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 502 through 504 No H-bonds generated for 'chain 'Y' and resid 502 through 504' Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 3.884A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 738 through 762 removed outlier: 3.904A pdb=" N ASN Y 742 " --> pdb=" O SER Y 738 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS Y 762 " --> pdb=" O HIS Y 758 " (cutoff:3.500A) Processing helix chain 'Y' and resid 783 through 787 Processing helix chain 'Y' and resid 790 through 802 removed outlier: 4.049A pdb=" N TYR Y 802 " --> pdb=" O ALA Y 798 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 892 Processing helix chain 'Y' and resid 897 through 904 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 3.747A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 945 through 950 Processing helix chain 'Y' and resid 965 through 978 removed outlier: 3.534A pdb=" N ARG Y 976 " --> pdb=" O ALA Y 972 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG Y 510 " --> pdb=" O GLU Y 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 33 through 34 removed outlier: 3.695A pdb=" N ARG Y 33 " --> pdb=" O ALA Y 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 518 through 519 removed outlier: 4.031A pdb=" N SER Y 518 " --> pdb=" O GLN Y 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 557 through 558 removed outlier: 4.036A pdb=" N ARG Y 557 " --> pdb=" O THR Y 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 669 through 670 removed outlier: 6.363A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA Y 769 " --> pdb=" O ILE Y 669 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU Y 766 " --> pdb=" O SER Y 812 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR Y 814 " --> pdb=" O LEU Y 766 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE Y 768 " --> pdb=" O THR Y 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 250 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 288 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 5.17 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: 1454 1.32 - 1.44: 3696 1.44 - 1.57: 5236 1.57 - 1.69: 323 1.69 - 1.81: 34 Bond restraints: 10743 Sorted by residual: bond pdb=" CA HIS Y 199 " pdb=" CB HIS Y 199 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.27e+00 bond pdb=" CA LEU Y 615 " pdb=" CB LEU Y 615 " ideal model delta sigma weight residual 1.531 1.449 0.082 3.28e-02 9.30e+02 6.18e+00 bond pdb=" CG LEU Y 585 " pdb=" CD1 LEU Y 585 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.95e+00 bond pdb=" C SER Y 197 " pdb=" N ILE Y 198 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.36e-02 5.41e+03 5.40e+00 bond pdb=" C ASN Y 501 " pdb=" N PRO Y 502 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.39e+00 ... (remaining 10738 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.95: 1031 105.95 - 113.00: 5814 113.00 - 120.05: 4044 120.05 - 127.09: 3967 127.09 - 134.14: 439 Bond angle restraints: 15295 Sorted by residual: angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 129.55 -16.37 2.37e+00 1.78e-01 4.77e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 125.99 -12.39 1.90e+00 2.77e-01 4.25e+01 angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.98 9.66 1.52e+00 4.33e-01 4.04e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 angle pdb=" N THR Y 954 " pdb=" CA THR Y 954 " pdb=" C THR Y 954 " ideal model delta sigma weight residual 114.62 109.13 5.49 1.14e+00 7.69e-01 2.32e+01 ... (remaining 15290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5739 34.22 - 68.44: 506 68.44 - 102.65: 46 102.65 - 136.87: 1 136.87 - 171.09: 4 Dihedral angle restraints: 6296 sinusoidal: 3639 harmonic: 2657 Sorted by residual: dihedral pdb=" CA ILE Y 198 " pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta harmonic sigma weight residual -180.00 -138.16 -41.84 0 5.00e+00 4.00e-02 7.00e+01 dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 232.00 64.29 167.71 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" CA GLY Y 367 " pdb=" C GLY Y 367 " pdb=" N VAL Y 368 " pdb=" CA VAL Y 368 " ideal model delta harmonic sigma weight residual -180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1507 0.068 - 0.137: 250 0.137 - 0.205: 48 0.205 - 0.273: 6 0.273 - 0.341: 5 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CB ILE Y 677 " pdb=" CA ILE Y 677 " pdb=" CG1 ILE Y 677 " pdb=" CG2 ILE Y 677 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' G B 30 " pdb=" C4' G B 30 " pdb=" O3' G B 30 " pdb=" C2' G B 30 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1813 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 534 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP Y 534 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 534 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 534 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 534 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 534 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 534 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " -0.039 2.00e-02 2.50e+03 1.85e-02 9.41e+00 pdb=" N9 A B 56 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A B 56 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 56 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO Y 502 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.040 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2340 2.78 - 3.31: 8487 3.31 - 3.84: 18053 3.84 - 4.37: 19591 4.37 - 4.90: 30769 Nonbonded interactions: 79240 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.251 2.440 nonbonded pdb=" O4 U B 65 " pdb=" O6 G B 87 " model vdw 2.295 2.432 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.302 2.440 nonbonded pdb=" O SER Y 204 " pdb=" OG SER Y 204 " model vdw 2.321 2.440 nonbonded pdb=" O SER Y 661 " pdb=" OG SER Y 661 " model vdw 2.334 2.440 ... (remaining 79235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.060 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.990 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.009 0.082 10743 Z= 0.566 Angle : 1.131 16.367 15295 Z= 0.624 Chirality : 0.056 0.341 1816 Planarity : 0.007 0.071 1364 Dihedral : 22.064 171.087 4569 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 16.88 % Favored : 82.48 % Rotamer: Outliers : 0.33 % Allowed : 11.51 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.84 (0.21), residues: 782 helix: -3.34 (0.18), residues: 349 sheet: -4.13 (0.40), residues: 101 loop : -4.32 (0.24), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP Y 534 HIS 0.019 0.004 HIS Y 250 PHE 0.039 0.004 PHE Y 609 TYR 0.022 0.003 TYR Y 732 ARG 0.003 0.000 ARG Y 787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.889 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.3214 time to fit residues: 37.2673 Evaluate side-chains 63 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 60 ASN Y 91 HIS Y 443 HIS Y 636 ASN Y 715 GLN ** Y 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 817 GLN Y 952 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10743 Z= 0.176 Angle : 0.667 9.476 15295 Z= 0.353 Chirality : 0.037 0.177 1816 Planarity : 0.005 0.047 1364 Dihedral : 22.618 174.927 3129 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 3.12 % Allowed : 16.61 % Favored : 80.26 % 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: -3.90 (0.27), residues: 782 helix: -1.22 (0.26), residues: 341 sheet: -3.85 (0.44), residues: 95 loop : -3.67 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Y 534 HIS 0.006 0.001 HIS Y 250 PHE 0.023 0.002 PHE Y 503 TYR 0.010 0.001 TYR Y 528 ARG 0.005 0.000 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.848 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 0.2408 time to fit residues: 31.3663 Evaluate side-chains 74 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0936 time to fit residues: 2.6577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 283 GLN Y 788 GLN Y 817 GLN Y 930 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10743 Z= 0.349 Angle : 0.748 11.620 15295 Z= 0.390 Chirality : 0.040 0.184 1816 Planarity : 0.005 0.045 1364 Dihedral : 22.620 170.434 3129 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.38 % Allowed : 16.11 % Favored : 83.50 % Rotamer: Outliers : 3.95 % Allowed : 21.38 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.30 (0.28), residues: 782 helix: -0.56 (0.28), residues: 340 sheet: -3.19 (0.52), residues: 91 loop : -3.66 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Y 534 HIS 0.007 0.002 HIS Y 91 PHE 0.021 0.002 PHE Y 775 TYR 0.019 0.002 TYR Y 575 ARG 0.003 0.000 ARG Y 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 0.888 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 88 average time/residue: 0.2136 time to fit residues: 27.5961 Evaluate side-chains 79 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1002 time to fit residues: 4.0950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 199 HIS ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10743 Z= 0.166 Angle : 0.619 8.120 15295 Z= 0.326 Chirality : 0.036 0.195 1816 Planarity : 0.004 0.042 1364 Dihedral : 22.494 175.392 3129 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 1.97 % Allowed : 23.19 % Favored : 74.84 % 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: -2.74 (0.30), residues: 782 helix: -0.03 (0.29), residues: 343 sheet: -3.10 (0.54), residues: 90 loop : -3.41 (0.28), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 534 HIS 0.008 0.001 HIS Y 285 PHE 0.024 0.002 PHE Y 775 TYR 0.009 0.001 TYR Y 83 ARG 0.002 0.000 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.864 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 0.2114 time to fit residues: 26.5955 Evaluate side-chains 71 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1163 time to fit residues: 2.2923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10743 Z= 0.356 Angle : 0.739 11.014 15295 Z= 0.383 Chirality : 0.040 0.184 1816 Planarity : 0.004 0.040 1364 Dihedral : 22.489 169.521 3129 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 16.37 % Favored : 83.25 % Rotamer: Outliers : 3.95 % Allowed : 23.68 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.71 (0.30), residues: 782 helix: -0.04 (0.29), residues: 344 sheet: -2.93 (0.55), residues: 91 loop : -3.41 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 534 HIS 0.007 0.002 HIS Y 91 PHE 0.032 0.003 PHE Y 775 TYR 0.022 0.002 TYR Y 575 ARG 0.002 0.000 ARG Y 628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 0.803 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 82 average time/residue: 0.2153 time to fit residues: 25.8312 Evaluate side-chains 78 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0951 time to fit residues: 3.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.0370 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 HIS Y 549 ASN Y 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10743 Z= 0.242 Angle : 0.665 9.586 15295 Z= 0.347 Chirality : 0.037 0.176 1816 Planarity : 0.004 0.040 1364 Dihedral : 22.457 170.242 3129 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.86 % Favored : 83.89 % Rotamer: Outliers : 2.14 % Allowed : 24.18 % Favored : 73.68 % 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: -2.46 (0.30), residues: 782 helix: 0.19 (0.29), residues: 344 sheet: -2.81 (0.56), residues: 91 loop : -3.30 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 91 PHE 0.034 0.002 PHE Y 775 TYR 0.014 0.002 TYR Y 575 ARG 0.002 0.000 ARG Y 787 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.861 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.2343 time to fit residues: 25.8806 Evaluate side-chains 71 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0902 time to fit residues: 2.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10743 Z= 0.241 Angle : 0.659 9.092 15295 Z= 0.343 Chirality : 0.037 0.175 1816 Planarity : 0.004 0.038 1364 Dihedral : 22.420 171.156 3129 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.47 % Favored : 84.27 % Rotamer: Outliers : 1.64 % Allowed : 25.16 % Favored : 73.19 % 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: -2.33 (0.30), residues: 782 helix: 0.32 (0.29), residues: 344 sheet: -2.74 (0.56), residues: 94 loop : -3.26 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 91 PHE 0.023 0.002 PHE Y 775 TYR 0.016 0.002 TYR Y 575 ARG 0.002 0.000 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.849 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2211 time to fit residues: 22.6880 Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1044 time to fit residues: 2.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 920 GLN Y 930 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10743 Z= 0.281 Angle : 0.686 9.978 15295 Z= 0.356 Chirality : 0.038 0.175 1816 Planarity : 0.004 0.038 1364 Dihedral : 22.425 169.272 3129 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.11 % Favored : 83.63 % Rotamer: Outliers : 0.66 % Allowed : 25.33 % Favored : 74.01 % 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: -2.30 (0.30), residues: 782 helix: 0.32 (0.29), residues: 344 sheet: -2.60 (0.59), residues: 86 loop : -3.25 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 534 HIS 0.005 0.002 HIS Y 91 PHE 0.018 0.002 PHE Y 609 TYR 0.017 0.002 TYR Y 575 ARG 0.002 0.000 ARG Y 787 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.838 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.2192 time to fit residues: 21.5322 Evaluate side-chains 61 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0967 time to fit residues: 1.5028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10743 Z= 0.188 Angle : 0.625 9.274 15295 Z= 0.326 Chirality : 0.035 0.179 1816 Planarity : 0.004 0.037 1364 Dihedral : 22.354 174.247 3129 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.09 % Favored : 84.65 % Rotamer: Outliers : 0.99 % Allowed : 26.32 % Favored : 72.70 % 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: -2.12 (0.31), residues: 782 helix: 0.56 (0.30), residues: 344 sheet: -2.90 (0.58), residues: 87 loop : -3.14 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 91 PHE 0.017 0.002 PHE Y 609 TYR 0.011 0.001 TYR Y 575 ARG 0.002 0.000 ARG Y 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.776 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.2427 time to fit residues: 24.9754 Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1017 time to fit residues: 1.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10743 Z= 0.186 Angle : 0.629 9.774 15295 Z= 0.327 Chirality : 0.036 0.178 1816 Planarity : 0.004 0.036 1364 Dihedral : 22.325 173.871 3129 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.86 % Favored : 84.02 % Rotamer: Outliers : 0.16 % Allowed : 27.80 % Favored : 72.04 % 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: -2.04 (0.31), residues: 782 helix: 0.66 (0.30), residues: 344 sheet: -2.89 (0.57), residues: 87 loop : -3.13 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 91 PHE 0.017 0.002 PHE Y 609 TYR 0.011 0.001 TYR Y 575 ARG 0.002 0.000 ARG Y 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.893 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.2152 time to fit residues: 21.0555 Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1019 time to fit residues: 1.2841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 85 optimal weight: 20.0000 chunk 35 optimal weight: 0.0670 chunk 87 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 283 GLN ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 933 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116988 restraints weight = 13992.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120517 restraints weight = 7570.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122861 restraints weight = 5182.972| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10743 Z= 0.152 Angle : 0.600 9.978 15295 Z= 0.312 Chirality : 0.034 0.183 1816 Planarity : 0.004 0.036 1364 Dihedral : 22.284 176.871 3129 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.58 % Favored : 85.29 % Rotamer: Outliers : 0.16 % Allowed : 28.29 % Favored : 71.55 % 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: -1.96 (0.31), residues: 782 helix: 0.73 (0.30), residues: 353 sheet: -2.90 (0.56), residues: 87 loop : -3.18 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 933 PHE 0.015 0.001 PHE Y 609 TYR 0.008 0.001 TYR Y 196 ARG 0.002 0.000 ARG Y 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.79 seconds wall clock time: 31 minutes 54.26 seconds (1914.26 seconds total)