Starting phenix.real_space_refine on Mon Mar 11 02:10:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/03_2024/8oif_16891_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 4237 2.51 5 N 1166 2.21 5 O 1165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 993": "OE1" <-> "OE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6589 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 4939 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 41, 'TRANS': 662} Chain breaks: 8 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 31, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 384 Chain: "I" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 560 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "L" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1067 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 132} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 4.26, per 1000 atoms: 0.65 Number of scatterers: 6589 At special positions: 0 Unit cell: (110.656, 118.317, 82.5664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 1165 8.00 N 1166 7.00 C 4237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS L 86 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 8 sheets defined 30.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 87 through 99 removed outlier: 4.417A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 267 through 270 No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 282 through 304 removed outlier: 4.145A pdb=" N HIS A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.722A pdb=" N GLU A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.723A pdb=" N GLU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.977A pdb=" N ARG A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.531A pdb=" N SER A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 854 through 871 removed outlier: 3.927A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.609A pdb=" N HIS A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 Processing helix chain 'I' and resid 104 through 115 Processing helix chain 'I' and resid 137 through 140 No H-bonds generated for 'chain 'I' and resid 137 through 140' Processing helix chain 'L' and resid 5 through 16 removed outlier: 3.650A pdb=" N GLU L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP L 13 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 123 through 131 removed outlier: 3.637A pdb=" N ASP L 127 " --> pdb=" O MET L 123 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 146 removed outlier: 3.577A pdb=" N GLU L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU L 142 " --> pdb=" O LYS L 138 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.555A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER A 58 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 37 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 60 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= C, first strand: chain 'A' and resid 892 through 896 removed outlier: 6.910A pdb=" N VAL A 535 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ALA A 562 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 537 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR A 564 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA A 536 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 436 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 463 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU A 437 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 465 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 904 through 906 Processing sheet with id= E, first strand: chain 'A' and resid 917 through 919 Processing sheet with id= F, first strand: chain 'A' and resid 993 through 995 removed outlier: 3.654A pdb=" N LEU A 946 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A 952 " --> pdb=" O HIS A 948 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 93 through 98 Processing sheet with id= H, first strand: chain 'L' and resid 37 through 39 removed outlier: 3.933A pdb=" N ALA L 37 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 53 " --> pdb=" O ALA L 37 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2169 1.34 - 1.46: 1537 1.46 - 1.58: 3014 1.58 - 1.70: 1 1.70 - 1.82: 27 Bond restraints: 6748 Sorted by residual: bond pdb=" CG PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.85e+00 bond pdb=" C LEU A 456 " pdb=" N GLY A 457 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.46e-02 4.69e+03 1.82e+00 bond pdb=" C4 AMP I 201 " pdb=" C5 AMP I 201 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" CB PRO A 382 " pdb=" CG PRO A 382 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.41e+00 bond pdb=" CA GLU A 113 " pdb=" CB GLU A 113 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.95e-01 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.47: 367 107.47 - 114.65: 3972 114.65 - 121.84: 3406 121.84 - 129.03: 1477 129.03 - 136.21: 58 Bond angle restraints: 9280 Sorted by residual: angle pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 112.00 106.39 5.61 1.40e+00 5.10e-01 1.61e+01 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 angle pdb=" CG1 ILE L 55 " pdb=" CB ILE L 55 " pdb=" CG2 ILE L 55 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" N GLU A 113 " pdb=" CA GLU A 113 " pdb=" C GLU A 113 " ideal model delta sigma weight residual 111.81 107.53 4.28 1.44e+00 4.82e-01 8.84e+00 angle pdb=" CB MET A 54 " pdb=" CG MET A 54 " pdb=" SD MET A 54 " ideal model delta sigma weight residual 112.70 119.83 -7.13 3.00e+00 1.11e-01 5.64e+00 ... (remaining 9275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 3753 23.94 - 47.87: 193 47.87 - 71.81: 10 71.81 - 95.75: 1 95.75 - 119.68: 1 Dihedral angle restraints: 3958 sinusoidal: 1265 harmonic: 2693 Sorted by residual: dihedral pdb=" C5' AMP I 201 " pdb=" O5' AMP I 201 " pdb=" P AMP I 201 " pdb=" O3P AMP I 201 " ideal model delta sinusoidal sigma weight residual -60.00 -179.68 119.68 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA HIS A 907 " pdb=" C HIS A 907 " pdb=" N HIS A 908 " pdb=" CA HIS A 908 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE A 906 " pdb=" C PHE A 906 " pdb=" N HIS A 907 " pdb=" CA HIS A 907 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 870 0.042 - 0.085: 206 0.085 - 0.127: 55 0.127 - 0.169: 1 0.169 - 0.211: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CB ILE L 55 " pdb=" CA ILE L 55 " pdb=" CG1 ILE L 55 " pdb=" CG2 ILE L 55 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE L 68 " pdb=" CA ILE L 68 " pdb=" CG1 ILE L 68 " pdb=" CG2 ILE L 68 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE L 55 " pdb=" N ILE L 55 " pdb=" C ILE L 55 " pdb=" CB ILE L 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1131 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 381 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 382 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 594 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO A 595 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 396 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.031 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1324 2.78 - 3.31: 5901 3.31 - 3.84: 10218 3.84 - 4.37: 10803 4.37 - 4.90: 20050 Nonbonded interactions: 48296 Sorted by model distance: nonbonded pdb=" OG1 THR I 125 " pdb=" OD1 ASN I 151 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR L 46 " pdb=" O TYR L 75 " model vdw 2.252 2.440 nonbonded pdb=" O THR A 927 " pdb=" OG SER A 930 " model vdw 2.259 2.440 nonbonded pdb=" OG SER I 112 " pdb=" O VAL I 117 " model vdw 2.280 2.440 nonbonded pdb=" O ASN A 527 " pdb=" OG SER A 530 " model vdw 2.302 2.440 ... (remaining 48291 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.250 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 23.070 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.003 0.059 6748 Z= 0.222 Angle : 0.595 9.327 9280 Z= 0.295 Chirality : 0.039 0.211 1134 Planarity : 0.006 0.115 1191 Dihedral : 13.828 119.684 2207 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 912 helix: 1.47 (0.31), residues: 316 sheet: -0.16 (0.45), residues: 137 loop : -1.65 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 PHE 0.009 0.001 PHE A 483 TYR 0.008 0.001 TYR A 596 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.808 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1287 time to fit residues: 7.3131 Evaluate side-chains 32 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 27 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6748 Z= 0.134 Angle : 0.514 6.866 9280 Z= 0.242 Chirality : 0.038 0.172 1134 Planarity : 0.005 0.075 1191 Dihedral : 5.139 81.674 989 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.00 % Allowed : 14.93 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 912 helix: 1.67 (0.31), residues: 316 sheet: -0.04 (0.44), residues: 146 loop : -1.57 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 554 PHE 0.007 0.001 PHE A1005 TYR 0.010 0.001 TYR A1010 ARG 0.001 0.000 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.775 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.5442 (t80) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.1467 time to fit residues: 9.9806 Evaluate side-chains 41 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6748 Z= 0.154 Angle : 0.520 8.932 9280 Z= 0.243 Chirality : 0.038 0.183 1134 Planarity : 0.005 0.065 1191 Dihedral : 4.602 53.885 989 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.16 % Allowed : 16.25 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.29), residues: 912 helix: 1.72 (0.31), residues: 316 sheet: -0.01 (0.44), residues: 146 loop : -1.58 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 907 PHE 0.006 0.001 PHE A1005 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.784 Fit side-chains REVERT: A 867 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 1005 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5484 (t80) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.1954 time to fit residues: 15.6288 Evaluate side-chains 46 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6748 Z= 0.155 Angle : 0.522 8.014 9280 Z= 0.243 Chirality : 0.038 0.168 1134 Planarity : 0.005 0.060 1191 Dihedral : 4.390 44.853 989 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.49 % Allowed : 16.92 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 912 helix: 1.73 (0.31), residues: 317 sheet: -0.17 (0.46), residues: 137 loop : -1.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.004 0.001 HIS A 286 PHE 0.005 0.001 PHE A1005 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.769 Fit side-chains REVERT: A 867 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 1005 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5509 (t80) outliers start: 15 outliers final: 10 residues processed: 50 average time/residue: 0.1355 time to fit residues: 10.5642 Evaluate side-chains 49 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6748 Z= 0.145 Angle : 0.511 7.663 9280 Z= 0.238 Chirality : 0.038 0.177 1134 Planarity : 0.004 0.054 1191 Dihedral : 4.199 45.607 989 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.32 % Allowed : 17.58 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 912 helix: 1.78 (0.32), residues: 317 sheet: 0.04 (0.45), residues: 146 loop : -1.54 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 PHE 0.005 0.001 PHE A 159 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.789 Fit side-chains REVERT: A 867 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 1005 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5475 (t80) outliers start: 14 outliers final: 11 residues processed: 49 average time/residue: 0.1476 time to fit residues: 11.2787 Evaluate side-chains 50 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 0.0570 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.250 Angle : 0.567 8.161 9280 Z= 0.270 Chirality : 0.040 0.166 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.561 45.628 989 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.65 % Allowed : 18.08 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 912 helix: 1.71 (0.31), residues: 311 sheet: -0.23 (0.47), residues: 121 loop : -1.63 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.006 0.001 HIS A 286 PHE 0.008 0.001 PHE A 389 TYR 0.008 0.001 TYR A 596 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 0.707 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5596 (t80) outliers start: 16 outliers final: 14 residues processed: 46 average time/residue: 0.1075 time to fit residues: 8.4040 Evaluate side-chains 47 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 98 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6748 Z= 0.154 Angle : 0.519 7.644 9280 Z= 0.243 Chirality : 0.038 0.168 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.286 46.047 989 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.32 % Allowed : 18.74 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 912 helix: 1.73 (0.31), residues: 317 sheet: -0.21 (0.47), residues: 121 loop : -1.59 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 PHE 0.006 0.001 PHE A 159 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.790 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.5524 (t80) outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 0.1365 time to fit residues: 10.7858 Evaluate side-chains 49 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.0370 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6748 Z= 0.133 Angle : 0.507 7.669 9280 Z= 0.236 Chirality : 0.038 0.166 1134 Planarity : 0.004 0.054 1191 Dihedral : 4.043 46.583 989 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.49 % Allowed : 18.91 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 912 helix: 1.86 (0.31), residues: 315 sheet: -0.00 (0.44), residues: 147 loop : -1.47 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 554 PHE 0.005 0.001 PHE A 159 TYR 0.006 0.000 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.729 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.5579 (t80) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.1344 time to fit residues: 10.4286 Evaluate side-chains 50 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.207 Angle : 0.544 8.489 9280 Z= 0.257 Chirality : 0.039 0.185 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.323 46.402 989 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.65 % Allowed : 18.74 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 912 helix: 1.85 (0.31), residues: 311 sheet: -0.28 (0.46), residues: 126 loop : -1.50 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 PHE 0.008 0.001 PHE A1005 TYR 0.007 0.001 TYR A 603 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.774 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.5630 (t80) outliers start: 16 outliers final: 13 residues processed: 49 average time/residue: 0.1071 time to fit residues: 8.9970 Evaluate side-chains 49 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 77 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6748 Z= 0.143 Angle : 0.512 8.089 9280 Z= 0.239 Chirality : 0.038 0.177 1134 Planarity : 0.004 0.056 1191 Dihedral : 4.096 46.958 989 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.49 % Allowed : 18.74 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 912 helix: 1.88 (0.31), residues: 315 sheet: -0.15 (0.43), residues: 153 loop : -1.50 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 907 PHE 0.005 0.001 PHE A 159 TYR 0.004 0.001 TYR A1010 ARG 0.001 0.000 ARG A 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.813 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5623 (t80) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.1285 time to fit residues: 10.2640 Evaluate side-chains 50 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 75 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 887 HIS A 891 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074147 restraints weight = 18442.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075595 restraints weight = 11039.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076509 restraints weight = 7955.346| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6748 Z= 0.140 Angle : 0.508 8.009 9280 Z= 0.237 Chirality : 0.038 0.177 1134 Planarity : 0.004 0.055 1191 Dihedral : 4.016 47.262 989 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.16 % Allowed : 19.24 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 912 helix: 1.91 (0.31), residues: 315 sheet: -0.13 (0.43), residues: 153 loop : -1.48 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.003 0.001 HIS A 554 PHE 0.006 0.001 PHE A 604 TYR 0.005 0.000 TYR A 603 ARG 0.001 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.79 seconds wall clock time: 28 minutes 52.53 seconds (1732.53 seconds total)