Starting phenix.real_space_refine on Mon Mar 11 05:06:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/03_2024/7fjq_31627_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4570 2.51 5 N 1203 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A PHE 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 1034": "NH1" <-> "NH2" Residue "A ARG 1072": "NH1" <-> "NH2" Residue "A TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1158": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7086 Unusual residues: {'SPM': 1} Classifications: {'peptide': 973, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 67, 'TRANS': 905, None: 1} Not linked: pdbres="PRO A1173 " pdbres="SPM A1201 " Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 260 Time building chain proxies: 4.20, per 1000 atoms: 0.59 Number of scatterers: 7086 At special positions: 0 Unit cell: (77.9509, 96.6152, 138.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1269 8.00 N 1203 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 317 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 36.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 117 through 123 Proline residue: A 121 - end of helix No H-bonds generated for 'chain 'A' and resid 117 through 123' Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.939A pdb=" N HIS A 198 " --> pdb=" O CYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.623A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.723A pdb=" N ALA A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 287 removed outlier: 4.197A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.743A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 423 No H-bonds generated for 'chain 'A' and resid 420 through 423' Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.850A pdb=" N VAL A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.534A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.610A pdb=" N ALA A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 555' Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.639A pdb=" N GLN A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 738 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 763 removed outlier: 3.545A pdb=" N VAL A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 841 through 843 No H-bonds generated for 'chain 'A' and resid 841 through 843' Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.846A pdb=" N CYS A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.390A pdb=" N LYS A 887 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 932 through 951 removed outlier: 3.522A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 978 removed outlier: 3.923A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1024 Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1079 through 1097 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1117 through 1139 Processing helix chain 'A' and resid 1158 through 1168 Processing sheet with id= A, first strand: chain 'A' and resid 338 through 341 removed outlier: 3.788A pdb=" N CYS A 338 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 340 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 352 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 493 through 495 Processing sheet with id= C, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.606A pdb=" N ARG A 745 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 512 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 747 " --> pdb=" O PHE A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 562 through 564 removed outlier: 3.730A pdb=" N LEU A 564 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 524 through 530 removed outlier: 3.647A pdb=" N ARG A 725 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 526 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 723 " --> pdb=" O MET A 526 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A 528 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 721 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 719 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 690 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 721 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 688 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A 723 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 686 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 641 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 642 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 623 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 773 through 775 removed outlier: 4.689A pdb=" N LEU A 773 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 874 through 876 removed outlier: 5.931A pdb=" N VAL A 891 " --> pdb=" O MET A 875 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 823 through 825 removed outlier: 7.521A pdb=" N LEU A 825 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 851 " --> pdb=" O LEU A 825 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 603 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: 2.06 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1025 1.25 - 1.39: 1712 1.39 - 1.53: 3693 1.53 - 1.67: 728 1.67 - 1.81: 65 Bond restraints: 7223 Sorted by residual: bond pdb=" CA TYR A 256 " pdb=" C TYR A 256 " ideal model delta sigma weight residual 1.523 1.308 0.215 1.34e-02 5.57e+03 2.57e+02 bond pdb=" CA HIS A 255 " pdb=" C HIS A 255 " ideal model delta sigma weight residual 1.523 1.347 0.176 1.34e-02 5.57e+03 1.73e+02 bond pdb=" CA ALA A 965 " pdb=" C ALA A 965 " ideal model delta sigma weight residual 1.524 1.363 0.161 1.27e-02 6.20e+03 1.60e+02 bond pdb=" C LEU A 964 " pdb=" O LEU A 964 " ideal model delta sigma weight residual 1.237 1.106 0.131 1.17e-02 7.31e+03 1.25e+02 bond pdb=" CA SER A 941 " pdb=" C SER A 941 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.17e+02 ... (remaining 7218 not shown) Histogram of bond angle deviations from ideal: 86.09 - 96.74: 7 96.74 - 107.39: 493 107.39 - 118.04: 5101 118.04 - 128.69: 4213 128.69 - 139.34: 56 Bond angle restraints: 9870 Sorted by residual: angle pdb=" N PRO A1172 " pdb=" CA PRO A1172 " pdb=" C PRO A1172 " ideal model delta sigma weight residual 110.70 86.09 24.61 1.22e+00 6.72e-01 4.07e+02 angle pdb=" N LYS A1117 " pdb=" CA LYS A1117 " pdb=" C LYS A1117 " ideal model delta sigma weight residual 111.71 98.66 13.05 1.15e+00 7.56e-01 1.29e+02 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 111.56 101.88 9.68 8.60e-01 1.35e+00 1.27e+02 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 111.11 123.97 -12.86 1.20e+00 6.94e-01 1.15e+02 angle pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" C LEU A1042 " ideal model delta sigma weight residual 109.81 133.44 -23.63 2.21e+00 2.05e-01 1.14e+02 ... (remaining 9865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3961 16.85 - 33.69: 266 33.69 - 50.53: 93 50.53 - 67.37: 17 67.37 - 84.22: 4 Dihedral angle restraints: 4341 sinusoidal: 1536 harmonic: 2805 Sorted by residual: dihedral pdb=" C LEU A1042 " pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual -122.60 -152.07 29.47 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual 122.80 151.73 -28.93 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual 122.80 147.79 -24.99 0 2.50e+00 1.60e-01 1.00e+02 ... (remaining 4338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1108 0.265 - 0.530: 82 0.530 - 0.795: 26 0.795 - 1.060: 4 1.060 - 1.325: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA LEU A1042 " pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CB LEU A1042 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.33 2.00e-01 2.50e+01 4.39e+01 chirality pdb=" CA GLN A 944 " pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CB GLN A 944 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LYS A 935 " pdb=" N LYS A 935 " pdb=" C LYS A 935 " pdb=" CB LYS A 935 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 1219 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " -0.040 2.00e-02 2.50e+03 7.67e-02 5.88e+01 pdb=" C ILE A 966 " 0.133 2.00e-02 2.50e+03 pdb=" O ILE A 966 " -0.047 2.00e-02 2.50e+03 pdb=" N ASP A 967 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 967 " -0.039 2.00e-02 2.50e+03 7.29e-02 5.31e+01 pdb=" C ASP A 967 " 0.126 2.00e-02 2.50e+03 pdb=" O ASP A 967 " -0.045 2.00e-02 2.50e+03 pdb=" N LEU A 968 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 969 " 0.032 2.00e-02 2.50e+03 6.23e-02 3.89e+01 pdb=" C VAL A 969 " -0.108 2.00e-02 2.50e+03 pdb=" O VAL A 969 " 0.039 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.036 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 152 2.56 - 3.15: 5556 3.15 - 3.73: 10859 3.73 - 4.32: 14301 4.32 - 4.90: 22852 Nonbonded interactions: 53720 Sorted by model distance: nonbonded pdb=" CB HIS A 255 " pdb=" N TYR A 256 " model vdw 1.980 2.816 nonbonded pdb=" CB TYR A 256 " pdb=" N TYR A 257 " model vdw 2.063 2.816 nonbonded pdb=" N SER A1055 " pdb=" OG SER A1055 " model vdw 2.181 2.496 nonbonded pdb=" O TYR A 256 " pdb=" N TRP A 258 " model vdw 2.204 2.520 nonbonded pdb=" O TYR A 256 " pdb=" C TYR A 257 " model vdw 2.294 3.270 ... (remaining 53715 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: 0.760 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: 3.270 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.200 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.019 0.215 7223 Z= 1.259 Angle : 2.025 24.610 9870 Z= 1.333 Chirality : 0.171 1.325 1222 Planarity : 0.014 0.144 1250 Dihedral : 13.671 84.216 2522 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % Rotamer: Outliers : 6.77 % Allowed : 9.94 % Favored : 83.29 % Cbeta Deviations : 4.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.24), residues: 953 helix: -1.36 (0.25), residues: 398 sheet: -2.71 (0.50), residues: 71 loop : -3.45 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1171 HIS 0.009 0.001 HIS A 255 PHE 0.066 0.004 PHE A 945 TYR 0.035 0.003 TYR A 940 ARG 0.003 0.001 ARG A1158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.8701 (pp) cc_final: 0.8493 (mm) REVERT: A 854 MET cc_start: 0.8812 (mmm) cc_final: 0.8491 (mmm) REVERT: A 918 MET cc_start: 0.8317 (ptp) cc_final: 0.7981 (ptp) REVERT: A 937 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mmt) REVERT: A 941 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (t) REVERT: A 942 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 1008 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (tt0) outliers start: 49 outliers final: 25 residues processed: 156 average time/residue: 0.1689 time to fit residues: 36.3085 Evaluate side-chains 95 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1080 PRO Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 88 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 219 ASN A 497 HIS A 870 GLN A1078 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7223 Z= 0.230 Angle : 0.800 8.892 9870 Z= 0.399 Chirality : 0.048 0.304 1222 Planarity : 0.008 0.132 1250 Dihedral : 9.242 57.527 1091 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.55 % Favored : 89.82 % Rotamer: Outliers : 5.25 % Allowed : 14.78 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -3.34 (0.25), residues: 953 helix: -1.36 (0.26), residues: 384 sheet: -1.64 (0.57), residues: 66 loop : -3.10 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1171 HIS 0.003 0.001 HIS A 255 PHE 0.020 0.002 PHE A 963 TYR 0.025 0.002 TYR A 936 ARG 0.005 0.001 ARG A1164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 81 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 MET cc_start: 0.8798 (mmm) cc_final: 0.8512 (mmm) REVERT: A 918 MET cc_start: 0.8283 (ptp) cc_final: 0.8076 (ptp) REVERT: A 920 ILE cc_start: 0.8927 (pp) cc_final: 0.8686 (pt) REVERT: A 937 MET cc_start: 0.8310 (tpp) cc_final: 0.7901 (mmm) REVERT: A 1047 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 1133 MET cc_start: 0.7102 (mmm) cc_final: 0.6864 (mmp) outliers start: 38 outliers final: 18 residues processed: 112 average time/residue: 0.1895 time to fit residues: 28.8719 Evaluate side-chains 84 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 50.0000 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7223 Z= 0.308 Angle : 0.767 10.142 9870 Z= 0.383 Chirality : 0.048 0.287 1222 Planarity : 0.006 0.078 1250 Dihedral : 8.074 59.450 1057 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.97 % Favored : 89.51 % Rotamer: Outliers : 4.97 % Allowed : 16.02 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -3.04 (0.25), residues: 953 helix: -1.08 (0.26), residues: 383 sheet: -1.20 (0.60), residues: 66 loop : -2.99 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1171 HIS 0.002 0.001 HIS A 822 PHE 0.022 0.002 PHE A 963 TYR 0.015 0.002 TYR A 871 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6278 (mm-30) REVERT: A 918 MET cc_start: 0.8366 (ptp) cc_final: 0.8142 (ptp) REVERT: A 1133 MET cc_start: 0.7276 (mmm) cc_final: 0.7016 (mmp) outliers start: 36 outliers final: 15 residues processed: 98 average time/residue: 0.1405 time to fit residues: 20.4592 Evaluate side-chains 78 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 0.0030 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7223 Z= 0.190 Angle : 0.699 10.284 9870 Z= 0.339 Chirality : 0.045 0.330 1222 Planarity : 0.006 0.107 1250 Dihedral : 7.439 59.295 1054 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.34 % Favored : 90.14 % Rotamer: Outliers : 3.87 % Allowed : 17.96 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.65 (0.26), residues: 953 helix: -0.68 (0.27), residues: 381 sheet: -0.94 (0.60), residues: 66 loop : -2.86 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1171 HIS 0.002 0.000 HIS A 413 PHE 0.013 0.001 PHE A 963 TYR 0.016 0.001 TYR A 936 ARG 0.003 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6410 (t80) cc_final: 0.5993 (t80) REVERT: A 169 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: A 1133 MET cc_start: 0.7202 (mmm) cc_final: 0.6949 (mmp) outliers start: 28 outliers final: 15 residues processed: 93 average time/residue: 0.1353 time to fit residues: 19.1260 Evaluate side-chains 81 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1116 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 0.0040 chunk 84 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7223 Z= 0.236 Angle : 0.713 10.730 9870 Z= 0.345 Chirality : 0.045 0.256 1222 Planarity : 0.006 0.098 1250 Dihedral : 6.825 54.575 1047 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.97 % Favored : 89.61 % Rotamer: Outliers : 5.11 % Allowed : 17.96 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.37 (0.27), residues: 953 helix: -0.37 (0.27), residues: 378 sheet: -0.66 (0.62), residues: 66 loop : -2.77 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1171 HIS 0.001 0.000 HIS A 255 PHE 0.014 0.001 PHE A 963 TYR 0.015 0.002 TYR A 166 ARG 0.003 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 69 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6281 (t80) cc_final: 0.5858 (t80) REVERT: A 169 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6143 (mp10) REVERT: A 1133 MET cc_start: 0.7251 (mmm) cc_final: 0.7010 (mmp) outliers start: 37 outliers final: 20 residues processed: 99 average time/residue: 0.1632 time to fit residues: 23.0454 Evaluate side-chains 87 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 55 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7223 Z= 0.176 Angle : 0.680 11.406 9870 Z= 0.327 Chirality : 0.044 0.218 1222 Planarity : 0.006 0.087 1250 Dihedral : 6.468 53.536 1047 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.60 % Favored : 90.98 % Rotamer: Outliers : 3.87 % Allowed : 19.48 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.09 (0.27), residues: 953 helix: -0.08 (0.28), residues: 378 sheet: -0.19 (0.70), residues: 56 loop : -2.66 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 643 HIS 0.001 0.000 HIS A 626 PHE 0.010 0.001 PHE A 963 TYR 0.019 0.001 TYR A 276 ARG 0.012 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 748 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7687 (ttp) REVERT: A 1133 MET cc_start: 0.7230 (mmm) cc_final: 0.6968 (mmp) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.1345 time to fit residues: 18.9240 Evaluate side-chains 87 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1135 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7223 Z= 0.257 Angle : 0.703 11.728 9870 Z= 0.340 Chirality : 0.045 0.245 1222 Planarity : 0.006 0.088 1250 Dihedral : 6.303 54.369 1045 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.65 % Favored : 89.93 % Rotamer: Outliers : 4.14 % Allowed : 20.03 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.93 (0.27), residues: 953 helix: 0.07 (0.28), residues: 377 sheet: -0.09 (0.73), residues: 56 loop : -2.58 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1171 HIS 0.002 0.000 HIS A 255 PHE 0.012 0.001 PHE A 963 TYR 0.013 0.001 TYR A 936 ARG 0.006 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6195 (t80) cc_final: 0.5941 (t80) REVERT: A 169 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6224 (mp10) REVERT: A 273 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 1133 MET cc_start: 0.7294 (mmm) cc_final: 0.7027 (mmp) outliers start: 30 outliers final: 23 residues processed: 93 average time/residue: 0.1532 time to fit residues: 22.0546 Evaluate side-chains 90 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1135 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7223 Z= 0.279 Angle : 0.715 12.717 9870 Z= 0.349 Chirality : 0.046 0.382 1222 Planarity : 0.006 0.085 1250 Dihedral : 6.207 55.397 1043 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.23 % Favored : 90.35 % Rotamer: Outliers : 4.28 % Allowed : 20.17 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.85 (0.27), residues: 953 helix: 0.14 (0.28), residues: 376 sheet: -0.08 (0.71), residues: 56 loop : -2.53 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1171 HIS 0.001 0.000 HIS A 255 PHE 0.011 0.001 PHE A 963 TYR 0.014 0.002 TYR A 166 ARG 0.006 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 69 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6142 (t80) cc_final: 0.5909 (t80) REVERT: A 169 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6229 (mp10) REVERT: A 1133 MET cc_start: 0.7308 (mmm) cc_final: 0.7046 (mmp) outliers start: 31 outliers final: 25 residues processed: 96 average time/residue: 0.1486 time to fit residues: 21.4108 Evaluate side-chains 92 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7223 Z= 0.186 Angle : 0.687 12.900 9870 Z= 0.329 Chirality : 0.045 0.364 1222 Planarity : 0.006 0.083 1250 Dihedral : 6.007 55.733 1043 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.81 % Favored : 90.77 % Rotamer: Outliers : 3.87 % Allowed : 20.58 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.69 (0.27), residues: 953 helix: 0.36 (0.29), residues: 376 sheet: 0.02 (0.69), residues: 56 loop : -2.52 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 643 HIS 0.001 0.000 HIS A 255 PHE 0.013 0.001 PHE A 375 TYR 0.013 0.001 TYR A 936 ARG 0.005 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 0.830 Fit side-chains REVERT: A 273 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 1133 MET cc_start: 0.7258 (mmm) cc_final: 0.6999 (mmp) outliers start: 28 outliers final: 22 residues processed: 91 average time/residue: 0.1383 time to fit residues: 18.9177 Evaluate side-chains 86 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7223 Z= 0.196 Angle : 0.699 13.212 9870 Z= 0.337 Chirality : 0.045 0.327 1222 Planarity : 0.006 0.083 1250 Dihedral : 5.930 55.308 1043 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.81 % Favored : 90.77 % Rotamer: Outliers : 3.45 % Allowed : 20.72 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.53 (0.28), residues: 953 helix: 0.50 (0.29), residues: 376 sheet: 0.16 (0.69), residues: 56 loop : -2.45 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 643 HIS 0.001 0.000 HIS A 413 PHE 0.023 0.001 PHE A 168 TYR 0.019 0.001 TYR A 166 ARG 0.005 0.000 ARG A 745 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 1.021 Fit side-chains REVERT: A 273 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 404 LYS cc_start: 0.7904 (tptt) cc_final: 0.7661 (tptp) REVERT: A 1133 MET cc_start: 0.7267 (mmm) cc_final: 0.7005 (mmp) outliers start: 25 outliers final: 22 residues processed: 87 average time/residue: 0.1320 time to fit residues: 17.7071 Evaluate side-chains 88 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 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 = 0.4225 r_free = 0.4225 target = 0.173826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104313 restraints weight = 10525.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106859 restraints weight = 6157.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108365 restraints weight = 4540.565| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7223 Z= 0.242 Angle : 0.711 13.575 9870 Z= 0.343 Chirality : 0.045 0.344 1222 Planarity : 0.006 0.082 1250 Dihedral : 6.006 55.471 1043 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.55 % Favored : 90.03 % Rotamer: Outliers : 3.87 % Allowed : 20.44 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 (0.28), residues: 953 helix: 0.46 (0.29), residues: 377 sheet: 0.31 (0.68), residues: 56 loop : -2.37 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1171 HIS 0.001 0.000 HIS A 626 PHE 0.012 0.001 PHE A 963 TYR 0.014 0.001 TYR A 936 ARG 0.005 0.000 ARG A 745 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.87 seconds wall clock time: 29 minutes 50.09 seconds (1790.09 seconds total)