Starting phenix.real_space_refine on Tue Feb 13 18:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/02_2024/6vp0_21302_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.145 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 14 5.49 5 S 44 5.16 5 C 4796 2.51 5 N 1146 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 127": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7210 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3353 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3353 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'3VV': 1, 'AV0': 1, 'POV': 2} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="POV C 601 " pdbres="P5S C 602 " Not linked: pdbres="P5S C 603 " pdbres="POV C 604 " Not linked: pdbres="POV C 604 " pdbres="3VV C 605 " Not linked: pdbres="3VV C 605 " pdbres="AV0 C 606 " Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'3VV': 1, 'AV0': 1, 'POV': 2} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="POV E 601 " pdbres="P5S E 602 " Not linked: pdbres="P5S E 603 " pdbres="POV E 604 " Not linked: pdbres="POV E 604 " pdbres="3VV E 605 " Not linked: pdbres="3VV E 605 " pdbres="AV0 E 606 " Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.57, per 1000 atoms: 0.63 Number of scatterers: 7210 At special positions: 0 Unit cell: (79.094, 123.654, 75.752, 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 44 16.00 P 14 15.00 O 1210 8.00 N 1146 7.00 C 4796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 73.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 86 through 114 removed outlier: 5.803A pdb=" N ARG C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 132 through 155 removed outlier: 4.713A pdb=" N ASN C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 185 Proline residue: C 179 - end of helix Processing helix chain 'C' and resid 193 through 222 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 275 through 306 removed outlier: 5.074A pdb=" N VAL C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 316 through 342 removed outlier: 3.877A pdb=" N LYS C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Proline residue: C 329 - end of helix Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 370 through 376 Processing helix chain 'C' and resid 379 through 388 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.168A pdb=" N VAL C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Proline residue: C 422 - end of helix Processing helix chain 'C' and resid 429 through 447 removed outlier: 4.191A pdb=" N ILE C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.576A pdb=" N ILE C 462 " --> pdb=" O TRP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 480 removed outlier: 3.861A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 86 through 114 removed outlier: 5.803A pdb=" N ARG E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 132 through 155 removed outlier: 4.713A pdb=" N ASN E 141 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 185 Proline residue: E 179 - end of helix Processing helix chain 'E' and resid 193 through 222 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 275 through 306 removed outlier: 5.074A pdb=" N VAL E 301 " --> pdb=" O GLN E 297 " (cutoff:3.500A) Proline residue: E 302 - end of helix Processing helix chain 'E' and resid 316 through 342 removed outlier: 3.877A pdb=" N LYS E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Proline residue: E 329 - end of helix Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 364 through 366 No H-bonds generated for 'chain 'E' and resid 364 through 366' Processing helix chain 'E' and resid 370 through 376 Processing helix chain 'E' and resid 379 through 388 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 400 through 423 removed outlier: 4.168A pdb=" N VAL E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Proline residue: E 422 - end of helix Processing helix chain 'E' and resid 429 through 447 removed outlier: 4.191A pdb=" N ILE E 438 " --> pdb=" O MET E 434 " (cutoff:3.500A) Proline residue: E 439 - end of helix Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.576A pdb=" N ILE E 462 " --> pdb=" O TRP E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 480 removed outlier: 3.861A pdb=" N TYR E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1182 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: 1.82 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1064 1.32 - 1.45: 2202 1.45 - 1.57: 4058 1.57 - 1.69: 26 1.69 - 1.82: 72 Bond restraints: 7422 Sorted by residual: bond pdb=" C49 3VV C 605 " pdb=" C50 3VV C 605 " ideal model delta sigma weight residual 1.291 1.527 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C49 3VV E 605 " pdb=" C50 3VV E 605 " ideal model delta sigma weight residual 1.291 1.527 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C49 3VV C 605 " pdb=" O48 3VV C 605 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C49 3VV E 605 " pdb=" O48 3VV E 605 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C47 3VV E 605 " pdb=" O48 3VV E 605 " ideal model delta sigma weight residual 1.286 1.446 -0.160 2.00e-02 2.50e+03 6.42e+01 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 67.40 - 80.73: 4 80.73 - 94.07: 8 94.07 - 107.41: 342 107.41 - 120.75: 7584 120.75 - 134.09: 2108 Bond angle restraints: 10046 Sorted by residual: angle pdb=" OG P5S E 603 " pdb=" P12 P5S E 603 " pdb=" O16 P5S E 603 " ideal model delta sigma weight residual 98.42 67.40 31.02 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OG P5S C 603 " pdb=" P12 P5S C 603 " pdb=" O16 P5S C 603 " ideal model delta sigma weight residual 98.42 67.42 31.00 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OG P5S E 602 " pdb=" P12 P5S E 602 " pdb=" O13 P5S E 602 " ideal model delta sigma weight residual 111.99 82.86 29.13 3.00e+00 1.11e-01 9.43e+01 angle pdb=" OG P5S C 602 " pdb=" P12 P5S C 602 " pdb=" O13 P5S C 602 " ideal model delta sigma weight residual 111.99 82.87 29.12 3.00e+00 1.11e-01 9.42e+01 angle pdb=" OG P5S C 602 " pdb=" P12 P5S C 602 " pdb=" O16 P5S C 602 " ideal model delta sigma weight residual 98.42 69.46 28.96 3.00e+00 1.11e-01 9.32e+01 ... (remaining 10041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 4256 35.38 - 70.76: 161 70.76 - 106.14: 21 106.14 - 141.52: 18 141.52 - 176.90: 4 Dihedral angle restraints: 4460 sinusoidal: 2052 harmonic: 2408 Sorted by residual: dihedral pdb=" O16 P5S E 603 " pdb=" C2 P5S E 603 " pdb=" C3 P5S E 603 " pdb=" O37 P5S E 603 " ideal model delta sinusoidal sigma weight residual -57.33 119.57 -176.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O16 P5S C 603 " pdb=" C2 P5S C 603 " pdb=" C3 P5S C 603 " pdb=" O37 P5S C 603 " ideal model delta sinusoidal sigma weight residual -57.33 119.52 -176.85 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O16 P5S C 602 " pdb=" C2 P5S C 602 " pdb=" C3 P5S C 602 " pdb=" O37 P5S C 602 " ideal model delta sinusoidal sigma weight residual 302.67 136.81 165.86 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 4457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 988 0.077 - 0.154: 66 0.154 - 0.231: 3 0.231 - 0.308: 5 0.308 - 0.385: 4 Chirality restraints: 1066 Sorted by residual: chirality pdb=" C31 3VV C 605 " pdb=" C29 3VV C 605 " pdb=" C33 3VV C 605 " pdb=" O32 3VV C 605 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C31 3VV E 605 " pdb=" C29 3VV E 605 " pdb=" C33 3VV E 605 " pdb=" O32 3VV E 605 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C50 3VV C 605 " pdb=" C49 3VV C 605 " pdb=" C52 3VV C 605 " pdb=" O51 3VV C 605 " both_signs ideal model delta sigma weight residual False -2.38 -2.70 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1063 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 3VV C 605 " -0.039 2.00e-02 2.50e+03 3.22e-02 1.29e+01 pdb=" C29 3VV C 605 " 0.018 2.00e-02 2.50e+03 pdb=" C31 3VV C 605 " -0.031 2.00e-02 2.50e+03 pdb=" N28 3VV C 605 " 0.048 2.00e-02 2.50e+03 pdb=" O30 3VV C 605 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV E 605 " 0.039 2.00e-02 2.50e+03 3.18e-02 1.27e+01 pdb=" C29 3VV E 605 " -0.018 2.00e-02 2.50e+03 pdb=" C31 3VV E 605 " 0.031 2.00e-02 2.50e+03 pdb=" N28 3VV E 605 " -0.048 2.00e-02 2.50e+03 pdb=" O30 3VV E 605 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 391 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 392 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 392 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 392 " 0.020 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2289 2.83 - 3.35: 6753 3.35 - 3.87: 11598 3.87 - 4.38: 13277 4.38 - 4.90: 23517 Nonbonded interactions: 57434 Sorted by model distance: nonbonded pdb=" NH2 ARG C 67 " pdb=" O HIS C 69 " model vdw 2.316 2.520 nonbonded pdb=" NH2 ARG E 67 " pdb=" O HIS E 69 " model vdw 2.316 2.520 nonbonded pdb=" N ASP C 245 " pdb=" OD1 ASP C 245 " model vdw 2.329 2.520 nonbonded pdb=" N ASP E 245 " pdb=" OD1 ASP E 245 " model vdw 2.329 2.520 nonbonded pdb=" ND1 HIS C 382 " pdb=" O39 3VV C 605 " model vdw 2.339 2.520 ... (remaining 57429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.940 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 : 0.011 0.236 7422 Z= 0.620 Angle : 1.374 31.024 10046 Z= 0.521 Chirality : 0.050 0.385 1066 Planarity : 0.004 0.034 1188 Dihedral : 21.078 176.902 2896 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.96 % Allowed : 14.57 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 800 helix: -0.13 (0.19), residues: 598 sheet: None (None), residues: 0 loop : -2.32 (0.35), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS C 201 PHE 0.009 0.001 PHE E 338 TYR 0.013 0.001 TYR E 339 ARG 0.001 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.775 Fit side-chains REVERT: C 89 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7317 (mp) REVERT: C 325 LYS cc_start: 0.8365 (mttt) cc_final: 0.8119 (mtmm) REVERT: C 359 GLU cc_start: 0.7678 (tp30) cc_final: 0.7400 (tp30) REVERT: C 362 ARG cc_start: 0.7449 (mtt180) cc_final: 0.7225 (mtp85) REVERT: C 374 TRP cc_start: 0.7945 (m100) cc_final: 0.7731 (m100) REVERT: C 389 PHE cc_start: 0.8617 (t80) cc_final: 0.7992 (t80) REVERT: C 416 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: E 89 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7317 (mp) REVERT: E 325 LYS cc_start: 0.8368 (mttt) cc_final: 0.8150 (mtmm) REVERT: E 359 GLU cc_start: 0.7678 (tp30) cc_final: 0.7401 (tp30) REVERT: E 362 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7224 (mtp85) REVERT: E 374 TRP cc_start: 0.7950 (m100) cc_final: 0.7743 (m100) REVERT: E 389 PHE cc_start: 0.8614 (t80) cc_final: 0.7993 (t80) REVERT: E 416 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6977 (tt0) outliers start: 14 outliers final: 6 residues processed: 152 average time/residue: 0.2715 time to fit residues: 51.0307 Evaluate side-chains 108 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 460 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN C 201 HIS C 246 ASN C 292 GLN E 149 GLN E 201 HIS E 246 ASN E 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7422 Z= 0.174 Angle : 0.514 5.308 10046 Z= 0.247 Chirality : 0.037 0.118 1066 Planarity : 0.004 0.042 1188 Dihedral : 20.863 168.656 1366 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.64 % Allowed : 17.37 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 800 helix: 1.48 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.88 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 442 HIS 0.004 0.001 HIS C 474 PHE 0.008 0.001 PHE C 338 TYR 0.013 0.001 TYR E 390 ARG 0.003 0.000 ARG E 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.747 Fit side-chains REVERT: C 359 GLU cc_start: 0.7772 (tp30) cc_final: 0.7543 (tp30) REVERT: C 362 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7250 (mtp85) REVERT: C 374 TRP cc_start: 0.7911 (m100) cc_final: 0.7653 (m100) REVERT: C 416 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: E 359 GLU cc_start: 0.7772 (tp30) cc_final: 0.7542 (tp30) REVERT: E 362 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7247 (mtp85) REVERT: E 374 TRP cc_start: 0.7922 (m100) cc_final: 0.7676 (m100) REVERT: E 416 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7046 (tt0) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.2516 time to fit residues: 38.9147 Evaluate side-chains 122 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 340 TRP Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 415 HIS C 465 GLN E 415 HIS E 465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7422 Z= 0.242 Angle : 0.526 5.405 10046 Z= 0.259 Chirality : 0.039 0.121 1066 Planarity : 0.004 0.040 1188 Dihedral : 19.696 168.161 1358 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 17.37 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 800 helix: 1.84 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.60 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS E 201 PHE 0.015 0.002 PHE E 389 TYR 0.012 0.001 TYR C 390 ARG 0.003 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.953 Fit side-chains REVERT: C 215 ASN cc_start: 0.8295 (m-40) cc_final: 0.8026 (m-40) REVERT: C 309 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7643 (mmtp) REVERT: C 325 LYS cc_start: 0.8407 (mttt) cc_final: 0.8164 (mtpt) REVERT: C 362 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7305 (mtp85) REVERT: C 416 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: C 446 ARG cc_start: 0.7863 (tpt170) cc_final: 0.7645 (tpt170) REVERT: E 106 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7456 (pt0) REVERT: E 215 ASN cc_start: 0.8291 (m-40) cc_final: 0.8026 (m-40) REVERT: E 309 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7634 (mmtp) REVERT: E 325 LYS cc_start: 0.8312 (mttt) cc_final: 0.8093 (mtpt) REVERT: E 362 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7305 (mtp85) REVERT: E 416 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: E 446 ARG cc_start: 0.7858 (tpt170) cc_final: 0.7643 (tpt170) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.2717 time to fit residues: 40.7634 Evaluate side-chains 130 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7422 Z= 0.303 Angle : 0.554 5.492 10046 Z= 0.272 Chirality : 0.040 0.122 1066 Planarity : 0.004 0.039 1188 Dihedral : 19.404 166.246 1358 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.48 % Allowed : 16.39 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.29), residues: 800 helix: 1.99 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 201 PHE 0.011 0.002 PHE E 338 TYR 0.012 0.002 TYR E 339 ARG 0.003 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.795 Fit side-chains REVERT: C 89 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7174 (mp) REVERT: C 125 LEU cc_start: 0.8733 (mt) cc_final: 0.8396 (mt) REVERT: C 330 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 362 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7421 (mtp85) REVERT: C 416 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: E 89 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7184 (mp) REVERT: E 125 LEU cc_start: 0.8744 (mt) cc_final: 0.8411 (mt) REVERT: E 330 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7211 (t0) REVERT: E 362 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7419 (mtp85) REVERT: E 416 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6990 (tt0) outliers start: 32 outliers final: 19 residues processed: 138 average time/residue: 0.2094 time to fit residues: 37.9206 Evaluate side-chains 134 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7422 Z= 0.284 Angle : 0.549 5.639 10046 Z= 0.269 Chirality : 0.039 0.121 1066 Planarity : 0.004 0.039 1188 Dihedral : 19.068 166.101 1358 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.20 % Allowed : 18.35 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.29), residues: 800 helix: 2.10 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS C 201 PHE 0.010 0.001 PHE E 338 TYR 0.011 0.001 TYR E 339 ARG 0.002 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.779 Fit side-chains REVERT: C 89 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7307 (mp) REVERT: C 125 LEU cc_start: 0.8748 (mt) cc_final: 0.8404 (mt) REVERT: C 309 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7623 (mmtp) REVERT: C 330 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7172 (t0) REVERT: C 362 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7380 (mtp85) REVERT: C 416 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: E 89 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7312 (mp) REVERT: E 125 LEU cc_start: 0.8757 (mt) cc_final: 0.8417 (mt) REVERT: E 309 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7610 (mmtp) REVERT: E 330 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 362 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7380 (mtp85) REVERT: E 416 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6904 (tt0) outliers start: 30 outliers final: 16 residues processed: 134 average time/residue: 0.2206 time to fit residues: 38.5232 Evaluate side-chains 136 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7422 Z= 0.143 Angle : 0.486 5.457 10046 Z= 0.238 Chirality : 0.037 0.115 1066 Planarity : 0.004 0.039 1188 Dihedral : 18.658 163.798 1358 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.10 % Allowed : 20.73 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.30), residues: 800 helix: 2.38 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.24 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.004 0.001 HIS E 474 PHE 0.010 0.001 PHE E 288 TYR 0.010 0.001 TYR C 243 ARG 0.002 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.758 Fit side-chains REVERT: C 89 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7283 (mp) REVERT: C 125 LEU cc_start: 0.8741 (mt) cc_final: 0.8347 (mt) REVERT: C 285 MET cc_start: 0.8088 (mtp) cc_final: 0.7822 (mtm) REVERT: C 309 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (mmtp) REVERT: C 337 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6664 (t80) REVERT: C 362 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7321 (mtp85) REVERT: C 416 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: E 89 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7283 (mp) REVERT: E 125 LEU cc_start: 0.8752 (mt) cc_final: 0.8362 (mt) REVERT: E 285 MET cc_start: 0.8089 (mtp) cc_final: 0.7823 (mtm) REVERT: E 309 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7635 (mmtp) REVERT: E 337 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6665 (t80) REVERT: E 362 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7324 (mtp85) REVERT: E 416 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: E 435 MET cc_start: 0.7896 (tpp) cc_final: 0.7690 (tpp) outliers start: 15 outliers final: 2 residues processed: 119 average time/residue: 0.2298 time to fit residues: 35.3981 Evaluate side-chains 114 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.0170 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7422 Z= 0.245 Angle : 0.539 5.566 10046 Z= 0.264 Chirality : 0.039 0.123 1066 Planarity : 0.004 0.039 1188 Dihedral : 18.573 162.427 1358 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.80 % Allowed : 20.73 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.30), residues: 800 helix: 2.33 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.003 0.001 HIS C 201 PHE 0.011 0.001 PHE C 288 TYR 0.012 0.001 TYR C 390 ARG 0.002 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.781 Fit side-chains REVERT: C 89 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7261 (mp) REVERT: C 125 LEU cc_start: 0.8728 (mt) cc_final: 0.8331 (mt) REVERT: C 285 MET cc_start: 0.8031 (mtp) cc_final: 0.7724 (mtm) REVERT: C 362 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7344 (mtp85) REVERT: C 416 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: E 89 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7257 (mp) REVERT: E 125 LEU cc_start: 0.8738 (mt) cc_final: 0.8347 (mt) REVERT: E 285 MET cc_start: 0.8031 (mtp) cc_final: 0.7726 (mtm) REVERT: E 362 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7346 (mtp85) REVERT: E 416 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6974 (tt0) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.2162 time to fit residues: 35.4663 Evaluate side-chains 126 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7422 Z= 0.171 Angle : 0.502 5.585 10046 Z= 0.245 Chirality : 0.037 0.115 1066 Planarity : 0.004 0.039 1188 Dihedral : 18.135 159.246 1358 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.22 % Allowed : 20.45 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.30), residues: 800 helix: 2.42 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.003 0.001 HIS E 474 PHE 0.012 0.001 PHE E 288 TYR 0.011 0.001 TYR E 390 ARG 0.001 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.748 Fit side-chains REVERT: C 89 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7405 (mp) REVERT: C 125 LEU cc_start: 0.8705 (mt) cc_final: 0.8306 (mt) REVERT: C 285 MET cc_start: 0.8031 (mtp) cc_final: 0.7727 (mtm) REVERT: C 337 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6677 (t80) REVERT: C 362 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7316 (mtp85) REVERT: C 416 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: E 89 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7416 (mp) REVERT: E 125 LEU cc_start: 0.8715 (mt) cc_final: 0.8319 (mt) REVERT: E 285 MET cc_start: 0.8031 (mtp) cc_final: 0.7730 (mtm) REVERT: E 337 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6642 (t80) REVERT: E 362 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7321 (mtp85) REVERT: E 416 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: E 435 MET cc_start: 0.7935 (tpp) cc_final: 0.7720 (tpp) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 0.2205 time to fit residues: 35.8571 Evaluate side-chains 123 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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: 0.7427 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7422 Z= 0.216 Angle : 0.521 5.594 10046 Z= 0.256 Chirality : 0.038 0.118 1066 Planarity : 0.004 0.040 1188 Dihedral : 17.986 156.440 1358 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.80 % Allowed : 21.15 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.30), residues: 800 helix: 2.39 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.09 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 442 HIS 0.003 0.001 HIS E 474 PHE 0.012 0.001 PHE C 447 TYR 0.011 0.001 TYR E 390 ARG 0.002 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.707 Fit side-chains REVERT: C 89 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7399 (mp) REVERT: C 123 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8994 (mt) REVERT: C 125 LEU cc_start: 0.8716 (mt) cc_final: 0.8325 (mt) REVERT: C 285 MET cc_start: 0.8012 (mtp) cc_final: 0.7691 (mtm) REVERT: C 337 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6664 (t80) REVERT: C 362 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7329 (mtp85) REVERT: C 416 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: E 89 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7396 (mp) REVERT: E 123 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8993 (mt) REVERT: E 125 LEU cc_start: 0.8725 (mt) cc_final: 0.8335 (mt) REVERT: E 285 MET cc_start: 0.8011 (mtp) cc_final: 0.7693 (mtm) REVERT: E 362 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7333 (mtp85) REVERT: E 416 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: E 435 MET cc_start: 0.7956 (tpp) cc_final: 0.7732 (tpp) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.2319 time to fit residues: 35.3032 Evaluate side-chains 125 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7422 Z= 0.218 Angle : 0.521 5.874 10046 Z= 0.256 Chirality : 0.038 0.118 1066 Planarity : 0.004 0.039 1188 Dihedral : 17.733 150.840 1358 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.52 % Allowed : 21.15 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.30), residues: 800 helix: 2.37 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.06 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 442 HIS 0.003 0.001 HIS C 474 PHE 0.021 0.001 PHE C 447 TYR 0.012 0.001 TYR C 390 ARG 0.002 0.000 ARG C 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.796 Fit side-chains REVERT: C 89 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7294 (mp) REVERT: C 123 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9014 (mt) REVERT: C 125 LEU cc_start: 0.8721 (mt) cc_final: 0.8343 (mt) REVERT: C 285 MET cc_start: 0.8005 (mtp) cc_final: 0.7688 (mtm) REVERT: C 309 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7702 (mmtp) REVERT: C 337 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6667 (t80) REVERT: C 416 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: E 89 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7294 (mp) REVERT: E 123 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9013 (mt) REVERT: E 125 LEU cc_start: 0.8732 (mt) cc_final: 0.8350 (mt) REVERT: E 285 MET cc_start: 0.8005 (mtp) cc_final: 0.7685 (mtm) REVERT: E 309 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7684 (mmtp) REVERT: E 416 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: E 447 PHE cc_start: 0.8797 (m-10) cc_final: 0.8580 (m-10) outliers start: 18 outliers final: 9 residues processed: 122 average time/residue: 0.2367 time to fit residues: 36.9680 Evaluate side-chains 121 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113361 restraints weight = 7784.543| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.19 r_work: 0.3091 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7422 Z= 0.183 Angle : 0.503 5.584 10046 Z= 0.247 Chirality : 0.037 0.115 1066 Planarity : 0.004 0.040 1188 Dihedral : 17.503 147.774 1358 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.52 % Allowed : 21.15 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.30), residues: 800 helix: 2.42 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 442 HIS 0.003 0.001 HIS C 474 PHE 0.017 0.001 PHE C 447 TYR 0.010 0.001 TYR C 390 ARG 0.001 0.000 ARG C 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.46 seconds wall clock time: 31 minutes 44.87 seconds (1904.87 seconds total)