Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 06:56:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/07_2023/7fjq_31627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/07_2023/7fjq_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_31627/07_2023/7fjq_31627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/07_2023/7fjq_31627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/07_2023/7fjq_31627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjq_31627/07_2023/7fjq_31627_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 3.96, per 1000 atoms: 0.56 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: 2.77 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: 1.25 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: 2.31 Time building geometry restraints manager: 3.01 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: 0.710 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: 3.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.880 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 156 average time/residue: 0.2081 time to fit residues: 44.9066 Evaluate side-chains 89 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.0692 time to fit residues: 4.1674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.5980 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: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 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: 0.7204 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7223 Z= 0.224 Angle : 0.798 9.589 9870 Z= 0.397 Chirality : 0.048 0.305 1222 Planarity : 0.008 0.135 1250 Dihedral : 6.519 38.464 1037 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.34 % Favored : 90.03 % Rotamer Outliers : 3.31 % 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: -3.35 (0.25), residues: 953 helix: -1.35 (0.26), residues: 385 sheet: -1.62 (0.57), residues: 66 loop : -3.13 (0.25), residues: 502 *********************** 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 105 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 100 average time/residue: 0.1951 time to fit residues: 26.4311 Evaluate side-chains 71 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1058 time to fit residues: 2.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.0970 chunk 27 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 40.0000 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 70 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: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 7223 Z= 0.232 Angle : 0.727 9.124 9870 Z= 0.362 Chirality : 0.047 0.300 1222 Planarity : 0.006 0.080 1250 Dihedral : 6.371 42.945 1037 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.97 % Favored : 89.51 % Rotamer Outliers : 2.76 % 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: -1.05 (0.26), residues: 382 sheet: -1.15 (0.60), residues: 66 loop : -3.03 (0.25), residues: 505 *********************** 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 89 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.784 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 86 average time/residue: 0.1629 time to fit residues: 20.4476 Evaluate side-chains 71 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0749 time to fit residues: 2.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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: 0.7253 moved from start: 0.3054 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= 0.220 Angle : 0.710 10.357 9870 Z= 0.346 Chirality : 0.045 0.319 1222 Planarity : 0.007 0.109 1250 Dihedral : 5.927 38.081 1037 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.65 % Favored : 89.82 % Rotamer Outliers : 1.80 % 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: -2.67 (0.26), residues: 953 helix: -0.68 (0.27), residues: 384 sheet: -0.91 (0.62), residues: 66 loop : -2.89 (0.25), residues: 503 *********************** 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 82 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 80 average time/residue: 0.1543 time to fit residues: 18.3299 Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1740 time to fit residues: 2.2689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 30.0000 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 7223 Z= 0.396 Angle : 0.797 11.005 9870 Z= 0.391 Chirality : 0.048 0.264 1222 Planarity : 0.007 0.101 1250 Dihedral : 6.188 40.220 1037 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.91 % Favored : 88.67 % Rotamer Outliers : 2.76 % 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: -2.53 (0.26), residues: 953 helix: -0.67 (0.27), residues: 382 sheet: -0.64 (0.63), residues: 66 loop : -2.74 (0.26), residues: 505 *********************** 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 89 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 86 average time/residue: 0.2206 time to fit residues: 26.6355 Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1004 time to fit residues: 2.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3608 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= 0.186 Angle : 0.711 11.374 9870 Z= 0.343 Chirality : 0.045 0.363 1222 Planarity : 0.006 0.104 1250 Dihedral : 5.740 37.663 1037 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.55 % Favored : 90.03 % Rotamer Outliers : 2.07 % 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: -2.21 (0.27), residues: 953 helix: -0.21 (0.28), residues: 378 sheet: -0.19 (0.68), residues: 56 loop : -2.72 (0.26), residues: 519 *********************** 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 82 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.728 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 0.1492 time to fit residues: 17.5834 Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0631 time to fit residues: 1.4843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7223 Z= 0.225 Angle : 0.712 11.969 9870 Z= 0.344 Chirality : 0.045 0.328 1222 Planarity : 0.006 0.103 1250 Dihedral : 5.630 37.651 1037 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.44 % Favored : 90.14 % Rotamer Outliers : 1.38 % 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: -2.03 (0.27), residues: 953 helix: -0.00 (0.28), residues: 379 sheet: -0.07 (0.69), residues: 56 loop : -2.67 (0.26), residues: 518 *********************** 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 81 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 80 average time/residue: 0.1617 time to fit residues: 18.9793 Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2022 time to fit residues: 2.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 18 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 chunk 8 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 81 optimal weight: 0.5980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 944 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3994 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= 0.172 Angle : 0.705 12.687 9870 Z= 0.337 Chirality : 0.045 0.282 1222 Planarity : 0.006 0.093 1250 Dihedral : 5.456 36.162 1037 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.50 % Favored : 91.08 % Rotamer Outliers : 0.83 % 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: -1.82 (0.27), residues: 953 helix: 0.29 (0.29), residues: 375 sheet: 0.04 (0.69), residues: 56 loop : -2.65 (0.25), residues: 522 *********************** 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 76 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.717 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.1389 time to fit residues: 16.0350 Evaluate side-chains 68 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0664 time to fit residues: 1.4667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7223 Z= 0.180 Angle : 0.705 13.123 9870 Z= 0.337 Chirality : 0.044 0.285 1222 Planarity : 0.006 0.094 1250 Dihedral : 5.344 36.094 1037 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.81 % Favored : 90.77 % Rotamer Outliers : 0.28 % 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: -1.67 (0.28), residues: 953 helix: 0.41 (0.29), residues: 382 sheet: 0.17 (0.70), residues: 56 loop : -2.60 (0.26), residues: 515 *********************** 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 70 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.822 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1516 time to fit residues: 16.0137 Evaluate side-chains 67 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0784 time to fit residues: 1.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4229 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 : 0.712 13.037 9870 Z= 0.339 Chirality : 0.045 0.268 1222 Planarity : 0.006 0.092 1250 Dihedral : 5.276 36.064 1037 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.02 % Favored : 90.56 % Rotamer Outliers : 0.41 % 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: -1.58 (0.28), residues: 953 helix: 0.49 (0.29), residues: 382 sheet: 0.21 (0.70), residues: 56 loop : -2.55 (0.26), residues: 515 ********************** 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 73 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.829 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 72 average time/residue: 0.1580 time to fit residues: 16.7685 Evaluate side-chains 66 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.179251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113756 restraints weight = 10563.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114682 restraints weight = 6416.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115636 restraints weight = 5321.777| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7223 Z= 0.212 Angle : 0.716 13.424 9870 Z= 0.343 Chirality : 0.045 0.270 1222 Planarity : 0.006 0.092 1250 Dihedral : 5.286 36.410 1037 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.13 % Favored : 90.45 % Rotamer Outliers : 0.55 % 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: -1.49 (0.28), residues: 953 helix: 0.53 (0.29), residues: 382 sheet: 0.18 (0.69), residues: 55 loop : -2.44 (0.26), residues: 516 =============================================================================== Job complete usr+sys time: 1507.49 seconds wall clock time: 28 minutes 17.54 seconds (1697.54 seconds total)