Starting phenix.real_space_refine on Mon Mar 11 06:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd6_24413/03_2024/7rd6_24413_updated.pdb" } resolution = 3.25 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= 0.002 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 36 5.16 5 Be 1 3.05 5 C 4760 2.51 5 N 1220 2.21 5 O 1375 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 167": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A ARG 930": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7396 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7396 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 929, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 902, None: 2} Not linked: pdbres="SER A1141 " pdbres="BEF A1201 " Not linked: pdbres="BEF A1201 " pdbres=" MG A1202 " Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.29, per 1000 atoms: 0.58 Number of scatterers: 7396 At special positions: 0 Unit cell: (78.47, 82.6, 140.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 Mg 1 11.99 F 3 9.00 O 1375 8.00 N 1220 7.00 C 4760 6.00 Be 1 4.00 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 6 sheets defined 44.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 197 through 210 removed outlier: 4.325A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 224 through 252 removed outlier: 3.823A pdb=" N SER A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 406 through 433 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 455 through 474 removed outlier: 4.156A pdb=" N ARG A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 531 through 540 removed outlier: 3.934A pdb=" N SER A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 667 through 670 No H-bonds generated for 'chain 'A' and resid 667 through 670' Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.711A pdb=" N GLU A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 757 through 765 Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 859 through 872 Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.842A pdb=" N VAL A 887 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER A 888 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 889 " --> pdb=" O ASP A 886 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS A 892 " --> pdb=" O MET A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 919 through 926 removed outlier: 3.596A pdb=" N THR A 922 " --> pdb=" O CYS A 919 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 925 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 926 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 960 Processing helix chain 'A' and resid 972 through 978 Processing helix chain 'A' and resid 983 through 991 removed outlier: 3.743A pdb=" N PHE A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 3.543A pdb=" N GLU A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A1010 " --> pdb=" O TYR A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1043 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 3.748A pdb=" N ALA A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1098 removed outlier: 3.753A pdb=" N ILE A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Proline residue: A1096 - end of helix Processing helix chain 'A' and resid 1110 through 1137 removed outlier: 3.677A pdb=" N SER A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Proline residue: A1126 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 155 through 157 removed outlier: 4.043A pdb=" N GLY A 350 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 354 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 275 through 279 removed outlier: 3.529A pdb=" N VAL A 278 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS A 383 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 290 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 299 through 302 Processing sheet with id= D, first strand: chain 'A' and resid 769 through 772 removed outlier: 6.864A pdb=" N VAL A 895 " --> pdb=" O CYS A 879 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLY A 881 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 897 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 913 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 523 through 526 removed outlier: 3.500A pdb=" N GLN A 514 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY A 747 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE A 518 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 745 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.570A pdb=" N HIS A 623 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 650 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL A 637 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLY A 648 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 659 " --> pdb=" O LEU A 702 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2334 1.34 - 1.46: 1150 1.46 - 1.57: 3998 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 7537 Sorted by residual: bond pdb=" BE BEF A1201 " pdb=" F2 BEF A1201 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" BE BEF A1201 " pdb=" F3 BEF A1201 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" BE BEF A1201 " pdb=" F1 BEF A1201 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" CB MET A 662 " pdb=" CG MET A 662 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C VAL A1095 " pdb=" N PRO A1096 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 7532 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.38: 82 104.38 - 111.84: 3683 111.84 - 119.29: 2615 119.29 - 126.75: 3750 126.75 - 134.21: 89 Bond angle restraints: 10219 Sorted by residual: angle pdb=" C TYR A 707 " pdb=" N GLU A 708 " pdb=" CA GLU A 708 " ideal model delta sigma weight residual 121.58 113.36 8.22 1.95e+00 2.63e-01 1.78e+01 angle pdb=" F2 BEF A1201 " pdb=" BE BEF A1201 " pdb=" F3 BEF A1201 " ideal model delta sigma weight residual 119.96 107.49 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CA LEU A 962 " pdb=" C LEU A 962 " pdb=" N PHE A 963 " ideal model delta sigma weight residual 118.59 125.29 -6.70 1.63e+00 3.76e-01 1.69e+01 angle pdb=" CB MET A 662 " pdb=" CG MET A 662 " pdb=" SD MET A 662 " ideal model delta sigma weight residual 112.70 100.86 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" F1 BEF A1201 " pdb=" BE BEF A1201 " pdb=" F3 BEF A1201 " ideal model delta sigma weight residual 120.12 109.48 10.64 3.00e+00 1.11e-01 1.26e+01 ... (remaining 10214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4013 17.29 - 34.59: 416 34.59 - 51.88: 71 51.88 - 69.18: 12 69.18 - 86.47: 10 Dihedral angle restraints: 4522 sinusoidal: 1789 harmonic: 2733 Sorted by residual: dihedral pdb=" CA TRP A 369 " pdb=" C TRP A 369 " pdb=" N ALA A 370 " pdb=" CA ALA A 370 " ideal model delta harmonic sigma weight residual 180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 661 " pdb=" C PHE A 661 " pdb=" N MET A 662 " pdb=" CA MET A 662 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS A 617 " pdb=" C HIS A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 825 0.043 - 0.085: 280 0.085 - 0.128: 93 0.128 - 0.171: 10 0.171 - 0.213: 3 Chirality restraints: 1211 Sorted by residual: chirality pdb=" CB THR A1108 " pdb=" CA THR A1108 " pdb=" OG1 THR A1108 " pdb=" CG2 THR A1108 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASP A1103 " pdb=" N ASP A1103 " pdb=" C ASP A1103 " pdb=" CB ASP A1103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1208 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 858 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 859 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 859 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 859 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 169 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ARG A 169 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG A 169 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 170 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 963 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C PHE A 963 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 963 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 964 " -0.010 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 415 2.73 - 3.27: 7515 3.27 - 3.81: 12309 3.81 - 4.36: 14888 4.36 - 4.90: 25376 Nonbonded interactions: 60503 Sorted by model distance: nonbonded pdb=" OD1 ASP A 776 " pdb=" N LYS A 777 " model vdw 2.183 2.520 nonbonded pdb=" OH TYR A 590 " pdb=" OE1 GLU A 605 " model vdw 2.241 2.440 nonbonded pdb=" O SER A 339 " pdb=" OH TYR A 386 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR A 311 " pdb=" OD1 ASN A 511 " model vdw 2.259 2.440 nonbonded pdb=" O ASN A 885 " pdb=" F1 BEF A1201 " model vdw 2.270 2.390 ... (remaining 60498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 5.060 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.004 0.085 7537 Z= 0.251 Angle : 0.789 12.469 10219 Z= 0.414 Chirality : 0.048 0.213 1211 Planarity : 0.004 0.050 1267 Dihedral : 14.648 86.474 2752 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -1.73 (0.27), residues: 919 helix: -0.39 (0.25), residues: 425 sheet: -1.75 (0.45), residues: 134 loop : -1.68 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 PHE 0.019 0.002 PHE A 987 TYR 0.026 0.002 TYR A 198 ARG 0.008 0.000 ARG A1135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6913 (tmm-80) REVERT: A 974 MET cc_start: 0.6267 (ttt) cc_final: 0.5979 (ttt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1830 time to fit residues: 31.3130 Evaluate side-chains 104 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7537 Z= 0.277 Angle : 0.653 7.586 10219 Z= 0.340 Chirality : 0.045 0.193 1211 Planarity : 0.004 0.043 1267 Dihedral : 5.021 24.013 1004 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.09 % Allowed : 9.42 % Favored : 89.49 % 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: -1.67 (0.27), residues: 919 helix: -0.29 (0.25), residues: 434 sheet: -1.80 (0.44), residues: 134 loop : -1.72 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.026 0.002 PHE A 228 TYR 0.019 0.002 TYR A 165 ARG 0.002 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.6942 (tmm-80) REVERT: A 632 TYR cc_start: 0.7606 (m-80) cc_final: 0.7319 (m-80) outliers start: 9 outliers final: 8 residues processed: 111 average time/residue: 0.1777 time to fit residues: 27.7446 Evaluate side-chains 102 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1068 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.184 Angle : 0.576 7.987 10219 Z= 0.304 Chirality : 0.043 0.140 1211 Planarity : 0.003 0.040 1267 Dihedral : 4.771 22.087 1004 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.45 % Allowed : 13.53 % Favored : 85.02 % 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: -1.49 (0.27), residues: 919 helix: -0.03 (0.25), residues: 432 sheet: -1.91 (0.46), residues: 121 loop : -1.73 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.009 0.001 HIS A 623 PHE 0.023 0.002 PHE A 661 TYR 0.021 0.001 TYR A 707 ARG 0.006 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.6897 (tmm-80) REVERT: A 632 TYR cc_start: 0.7516 (m-80) cc_final: 0.7284 (m-80) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.1727 time to fit residues: 27.5229 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 795 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.195 Angle : 0.583 8.919 10219 Z= 0.306 Chirality : 0.043 0.165 1211 Planarity : 0.003 0.041 1267 Dihedral : 4.684 21.780 1004 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.81 % Allowed : 16.06 % Favored : 82.13 % 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: -1.40 (0.27), residues: 919 helix: 0.05 (0.25), residues: 432 sheet: -1.86 (0.45), residues: 121 loop : -1.69 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.007 0.001 HIS A 623 PHE 0.017 0.002 PHE A 987 TYR 0.021 0.001 TYR A 707 ARG 0.003 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.841 Fit side-chains REVERT: A 389 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.6865 (tmm-80) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.1828 time to fit residues: 28.4888 Evaluate side-chains 105 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7537 Z= 0.162 Angle : 0.562 7.835 10219 Z= 0.297 Chirality : 0.042 0.171 1211 Planarity : 0.003 0.042 1267 Dihedral : 4.516 20.879 1004 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.69 % Allowed : 17.39 % Favored : 80.92 % 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: -1.28 (0.27), residues: 919 helix: 0.20 (0.25), residues: 430 sheet: -1.85 (0.45), residues: 122 loop : -1.69 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.002 0.001 HIS A 945 PHE 0.021 0.001 PHE A 661 TYR 0.020 0.001 TYR A 707 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.867 Fit side-chains REVERT: A 389 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6769 (tmm-80) REVERT: A 498 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6738 (mt-10) REVERT: A 670 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.4881 (mtt) REVERT: A 1053 MET cc_start: 0.7094 (ppp) cc_final: 0.6883 (ppp) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.1614 time to fit residues: 27.3570 Evaluate side-chains 114 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7537 Z= 0.171 Angle : 0.570 8.722 10219 Z= 0.298 Chirality : 0.043 0.298 1211 Planarity : 0.003 0.041 1267 Dihedral : 4.464 22.862 1004 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.93 % Allowed : 19.08 % Favored : 78.99 % 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: -1.24 (0.27), residues: 919 helix: 0.24 (0.25), residues: 432 sheet: -1.84 (0.45), residues: 122 loop : -1.66 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 PHE 0.016 0.001 PHE A 987 TYR 0.018 0.001 TYR A 447 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.833 Fit side-chains REVERT: A 389 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6692 (tmm-80) REVERT: A 636 GLN cc_start: 0.6840 (pp30) cc_final: 0.6600 (pp30) REVERT: A 670 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5023 (mtt) REVERT: A 856 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6752 (ttm110) outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.1812 time to fit residues: 29.5838 Evaluate side-chains 111 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A1036 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7537 Z= 0.243 Angle : 0.620 7.733 10219 Z= 0.323 Chirality : 0.044 0.291 1211 Planarity : 0.003 0.043 1267 Dihedral : 4.708 23.545 1004 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.29 % Allowed : 19.32 % Favored : 78.38 % 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: -1.43 (0.27), residues: 919 helix: 0.11 (0.25), residues: 430 sheet: -2.17 (0.42), residues: 132 loop : -1.67 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 PHE 0.018 0.002 PHE A 661 TYR 0.018 0.002 TYR A 447 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.952 Fit side-chains REVERT: A 389 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.6712 (tmm-80) REVERT: A 482 GLU cc_start: 0.7717 (tt0) cc_final: 0.7386 (tm-30) REVERT: A 663 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: A 670 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5160 (mtt) REVERT: A 856 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6708 (ttm110) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1759 time to fit residues: 29.0136 Evaluate side-chains 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 795 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7537 Z= 0.183 Angle : 0.582 7.664 10219 Z= 0.303 Chirality : 0.043 0.282 1211 Planarity : 0.003 0.046 1267 Dihedral : 4.590 24.267 1004 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.66 % Allowed : 19.44 % Favored : 77.90 % 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: -1.33 (0.27), residues: 919 helix: 0.23 (0.25), residues: 430 sheet: -2.07 (0.43), residues: 132 loop : -1.69 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 PHE 0.014 0.001 PHE A 987 TYR 0.019 0.001 TYR A 447 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.810 Fit side-chains REVERT: A 389 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.6695 (tmm-80) REVERT: A 662 MET cc_start: 0.5956 (tpp) cc_final: 0.5750 (tpp) REVERT: A 663 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: A 670 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4943 (mtt) REVERT: A 856 ARG cc_start: 0.7320 (mtp85) cc_final: 0.6833 (ttm110) REVERT: A 872 MET cc_start: 0.6373 (mmp) cc_final: 0.6155 (mmp) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.1878 time to fit residues: 32.1300 Evaluate side-chains 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7537 Z= 0.161 Angle : 0.571 7.303 10219 Z= 0.296 Chirality : 0.042 0.273 1211 Planarity : 0.003 0.046 1267 Dihedral : 4.415 24.631 1004 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.29 % Allowed : 20.05 % Favored : 77.66 % 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: -1.21 (0.27), residues: 919 helix: 0.30 (0.25), residues: 431 sheet: -1.80 (0.44), residues: 124 loop : -1.70 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 PHE 0.014 0.001 PHE A 987 TYR 0.023 0.001 TYR A 447 ARG 0.001 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.845 Fit side-chains REVERT: A 250 GLU cc_start: 0.5673 (tm-30) cc_final: 0.4580 (mm-30) REVERT: A 271 LYS cc_start: 0.7095 (mptt) cc_final: 0.5805 (tptt) REVERT: A 277 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7629 (ttpp) REVERT: A 389 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6586 (tmm-80) REVERT: A 513 MET cc_start: 0.8404 (ptp) cc_final: 0.8018 (mtm) REVERT: A 662 MET cc_start: 0.5893 (tpp) cc_final: 0.5610 (tpp) REVERT: A 663 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.5619 (tm-30) REVERT: A 670 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.5007 (mtt) REVERT: A 842 PHE cc_start: 0.6037 (t80) cc_final: 0.5734 (t80) REVERT: A 856 ARG cc_start: 0.7313 (mtp85) cc_final: 0.6847 (ttm110) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.1828 time to fit residues: 29.8274 Evaluate side-chains 114 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7537 Z= 0.165 Angle : 0.583 7.405 10219 Z= 0.302 Chirality : 0.042 0.274 1211 Planarity : 0.003 0.048 1267 Dihedral : 4.401 24.759 1004 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.17 % Allowed : 20.53 % Favored : 77.29 % 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: -1.17 (0.27), residues: 919 helix: 0.32 (0.25), residues: 431 sheet: -1.73 (0.45), residues: 124 loop : -1.71 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 PHE 0.014 0.001 PHE A 987 TYR 0.027 0.001 TYR A 447 ARG 0.003 0.000 ARG A 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.859 Fit side-chains REVERT: A 250 GLU cc_start: 0.5588 (tm-30) cc_final: 0.4559 (mm-30) REVERT: A 271 LYS cc_start: 0.7211 (mptt) cc_final: 0.5920 (tptt) REVERT: A 277 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7651 (ttpp) REVERT: A 371 ASN cc_start: 0.7507 (m-40) cc_final: 0.7281 (m-40) REVERT: A 389 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6668 (tmm-80) REVERT: A 482 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 513 MET cc_start: 0.8338 (ptp) cc_final: 0.7995 (mtm) REVERT: A 662 MET cc_start: 0.5883 (tpp) cc_final: 0.5646 (tpp) REVERT: A 663 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: A 670 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.4923 (mtt) REVERT: A 856 ARG cc_start: 0.7319 (mtp85) cc_final: 0.6856 (ttm110) outliers start: 18 outliers final: 16 residues processed: 118 average time/residue: 0.1738 time to fit residues: 28.8659 Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.191574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154567 restraints weight = 7868.534| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.26 r_work: 0.3921 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7537 Z= 0.201 Angle : 0.611 7.666 10219 Z= 0.315 Chirality : 0.043 0.276 1211 Planarity : 0.003 0.051 1267 Dihedral : 4.492 24.444 1004 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.29 % Allowed : 20.41 % Favored : 77.29 % 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: -1.14 (0.27), residues: 919 helix: 0.35 (0.25), residues: 427 sheet: -1.80 (0.45), residues: 127 loop : -1.63 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 PHE 0.015 0.001 PHE A 987 TYR 0.028 0.001 TYR A 447 ARG 0.002 0.000 ARG A 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.31 seconds wall clock time: 32 minutes 51.64 seconds (1971.64 seconds total)