Starting phenix.real_space_refine on Tue Jun 17 08:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvm_47211/06_2025/9dvm_47211_trim.cif" } resolution = 2.92 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= 0.010 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 42 5.16 5 C 6508 2.51 5 N 1583 2.21 5 O 1780 1.98 5 H 9572 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19525 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 9602 Classifications: {'peptide': 578} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 4 Chain: "B" Number of atoms: 9555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 9555 Classifications: {'peptide': 574} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain breaks: 4 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.03, per 1000 atoms: 0.62 Number of scatterers: 19525 At special positions: 0 Unit cell: (96.425, 100.05, 125.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 40 15.00 O 1780 8.00 N 1583 7.00 C 6508 6.00 H 9572 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 6.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 83.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.371A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 47 through 98 Processing helix chain 'A' and resid 126 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.584A pdb=" N ALA A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 227 " --> pdb=" O GLY A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.502A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.646A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.065A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 445 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 473 through 502 removed outlier: 4.282A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 582 removed outlier: 3.932A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 623 Proline residue: A 598 - end of helix removed outlier: 3.539A pdb=" N ASN A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.770A pdb=" N HIS B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.275A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 47 through 98 Processing helix chain 'B' and resid 123 through 168 Processing helix chain 'B' and resid 170 through 179 removed outlier: 4.079A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.549A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 268 through 296 removed outlier: 5.241A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.576A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.142A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.016A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.595A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.074A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix 731 hydrogen bonds defined for protein. 2166 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: 7.73 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9552 1.03 - 1.23: 105 1.23 - 1.43: 4320 1.43 - 1.62: 5742 1.62 - 1.82: 80 Bond restraints: 19799 Sorted by residual: bond pdb=" O45 I8P B 704 " pdb=" PB5 I8P B 704 " ideal model delta sigma weight residual 1.695 1.583 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" O45 I8P B 705 " pdb=" PB5 I8P B 705 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" O45 I8P A 705 " pdb=" PB5 I8P A 705 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O45 I8P A 704 " pdb=" PB5 I8P A 704 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" O3P CPL B 707 " pdb=" P CPL B 707 " ideal model delta sigma weight residual 1.633 1.739 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 19794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 35269 3.05 - 6.11: 167 6.11 - 9.16: 71 9.16 - 12.21: 20 12.21 - 15.26: 18 Bond angle restraints: 35545 Sorted by residual: angle pdb=" O1P CPL B 707 " pdb=" P CPL B 707 " pdb=" O2P CPL B 707 " ideal model delta sigma weight residual 119.55 134.81 -15.26 3.00e+00 1.11e-01 2.59e+01 angle pdb=" O1P CPL A 707 " pdb=" P CPL A 707 " pdb=" O2P CPL A 707 " ideal model delta sigma weight residual 119.55 134.73 -15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" O65 I8P A 704 " pdb=" PB5 I8P A 704 " pdb=" O75 I8P A 704 " ideal model delta sigma weight residual 113.85 99.79 14.06 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O65 I8P B 705 " pdb=" PB5 I8P B 705 " pdb=" O75 I8P B 705 " ideal model delta sigma weight residual 113.85 99.82 14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O65 I8P A 705 " pdb=" PB5 I8P A 705 " pdb=" O75 I8P A 705 " ideal model delta sigma weight residual 113.85 99.82 14.03 3.00e+00 1.11e-01 2.19e+01 ... (remaining 35540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 9243 35.85 - 71.70: 355 71.70 - 107.55: 22 107.55 - 143.40: 11 143.40 - 179.25: 4 Dihedral angle restraints: 9635 sinusoidal: 5203 harmonic: 4432 Sorted by residual: dihedral pdb=" O2 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C2 CPL A 707 " pdb=" O3P CPL A 707 " ideal model delta sinusoidal sigma weight residual -50.82 128.43 -179.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C2 CPL A 707 " pdb=" O3P CPL A 707 " ideal model delta sinusoidal sigma weight residual 72.09 -110.82 -177.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O35 I8P B 705 " pdb=" O45 I8P B 705 " pdb=" PA5 I8P B 705 " pdb=" PB5 I8P B 705 " ideal model delta sinusoidal sigma weight residual -10.77 163.19 -173.96 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1361 0.071 - 0.143: 113 0.143 - 0.214: 12 0.214 - 0.286: 2 0.286 - 0.357: 8 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C17 CLR A 706 " pdb=" C13 CLR A 706 " pdb=" C16 CLR A 706 " pdb=" C20 CLR A 706 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C17 CLR B 706 " pdb=" C13 CLR B 706 " pdb=" C16 CLR B 706 " pdb=" C20 CLR B 706 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C2 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C3 CPL A 707 " pdb=" O2 CPL A 707 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 1493 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 604 " 0.339 9.50e-02 1.11e+02 1.60e-01 3.05e+02 pdb=" NE ARG A 604 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 604 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 604 " 0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG A 604 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG A 604 " -0.230 2.00e-02 2.50e+03 pdb="HH12 ARG A 604 " 0.222 2.00e-02 2.50e+03 pdb="HH21 ARG A 604 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 604 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 482 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" N TYR A 483 " -0.051 2.00e-02 2.50e+03 pdb=" CA TYR A 483 " 0.013 2.00e-02 2.50e+03 pdb=" H TYR A 483 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 482 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C LYS A 482 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 482 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 483 " 0.014 2.00e-02 2.50e+03 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 296 2.09 - 2.72: 31892 2.72 - 3.35: 60366 3.35 - 3.97: 73540 3.97 - 4.60: 115586 Nonbonded interactions: 281680 Sorted by model distance: nonbonded pdb=" HG SER B 402 " pdb=" HG2 ARG B 604 " model vdw 1.463 2.270 nonbonded pdb="HD11 LEU B 77 " pdb=" HD2 LYS B 190 " model vdw 1.606 2.440 nonbonded pdb=" HH TYR A 559 " pdb=" OE2 GLU A 613 " model vdw 1.621 2.450 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.624 2.450 nonbonded pdb=" O LYS B 482 " pdb=" HG1 THR B 485 " model vdw 1.635 2.450 ... (remaining 281675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 625 or resid 701 through 707)) selection = (chain 'B' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE or name NZ or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 \ or name HZ1 or name HZ2 or name HZ3)) or resid 3 through 25 or (resid 26 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HZ2)) or resid 27 throu \ gh 98 or (resid 125 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB2 or n \ ame HB3 or name HD2 or name HE1 or name HE2)) or resid 126 through 157 or (resid \ 158 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1)) or res \ id 159 through 625 or resid 701 through 707)) } 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: 3.630 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: 0.350 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 48.740 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.006 0.112 10229 Z= 0.324 Angle : 1.059 15.264 13913 Z= 0.415 Chirality : 0.046 0.357 1496 Planarity : 0.004 0.086 1662 Dihedral : 19.907 179.254 3989 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.39 % Allowed : 20.06 % Favored : 79.55 % 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: 3.67 (0.26), residues: 1132 helix: 3.31 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.002 0.000 HIS B 441 PHE 0.013 0.001 PHE B 610 TYR 0.030 0.001 TYR B 352 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.10775 ( 731) hydrogen bonds : angle 4.79997 ( 2166) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.85144 ( 4) covalent geometry : bond 0.00632 (10227) covalent geometry : angle 1.05933 (13909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.7623 (t80) cc_final: 0.7261 (m-80) REVERT: A 417 TYR cc_start: 0.7227 (t80) cc_final: 0.5831 (m-80) REVERT: A 471 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6969 (tppt) REVERT: B 71 THR cc_start: 0.7779 (t) cc_final: 0.7457 (m) REVERT: B 369 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8155 (mmpt) outliers start: 4 outliers final: 4 residues processed: 209 average time/residue: 2.5164 time to fit residues: 567.4898 Evaluate side-chains 134 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 515 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 204 ASN A 401 ASN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.184356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143228 restraints weight = 27596.397| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.46 r_work: 0.3133 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10229 Z= 0.167 Angle : 0.553 7.106 13913 Z= 0.282 Chirality : 0.036 0.230 1496 Planarity : 0.004 0.050 1662 Dihedral : 17.095 176.309 1752 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.77 % Allowed : 21.63 % Favored : 76.60 % 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: 3.53 (0.25), residues: 1132 helix: 3.17 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 PHE 0.028 0.002 PHE A 605 TYR 0.011 0.001 TYR B 483 ARG 0.008 0.001 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 731) hydrogen bonds : angle 4.15768 ( 2166) SS BOND : bond 0.00295 ( 2) SS BOND : angle 0.98839 ( 4) covalent geometry : bond 0.00374 (10227) covalent geometry : angle 0.55258 (13909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 197 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: A 283 PHE cc_start: 0.8114 (t80) cc_final: 0.7423 (m-80) REVERT: A 417 TYR cc_start: 0.7530 (t80) cc_final: 0.5722 (m-80) REVERT: B 71 THR cc_start: 0.7732 (t) cc_final: 0.7466 (m) REVERT: B 75 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: B 318 GLU cc_start: 0.8535 (tt0) cc_final: 0.8307 (tt0) REVERT: B 443 TYR cc_start: 0.7696 (m-80) cc_final: 0.7483 (m-80) REVERT: B 590 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6936 (t70) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 2.1224 time to fit residues: 336.0118 Evaluate side-chains 136 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137017 restraints weight = 27420.021| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.41 r_work: 0.3325 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10229 Z= 0.150 Angle : 0.512 8.406 13913 Z= 0.263 Chirality : 0.035 0.241 1496 Planarity : 0.004 0.043 1662 Dihedral : 15.969 171.848 1750 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 20.65 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.25), residues: 1132 helix: 3.04 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 PHE 0.023 0.001 PHE A 605 TYR 0.011 0.001 TYR A 352 ARG 0.006 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 731) hydrogen bonds : angle 4.02768 ( 2166) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.17979 ( 4) covalent geometry : bond 0.00331 (10227) covalent geometry : angle 0.51196 (13909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8658 (tp) REVERT: A 193 GLN cc_start: 0.8125 (tp40) cc_final: 0.7913 (tp-100) REVERT: A 197 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: A 283 PHE cc_start: 0.8179 (t80) cc_final: 0.7553 (m-80) REVERT: A 417 TYR cc_start: 0.7562 (t80) cc_final: 0.5852 (m-80) REVERT: B 71 THR cc_start: 0.7821 (t) cc_final: 0.7511 (m) REVERT: B 369 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8550 (mmtt) REVERT: B 443 TYR cc_start: 0.7715 (m-80) cc_final: 0.7478 (m-80) REVERT: B 590 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7126 (t70) outliers start: 21 outliers final: 11 residues processed: 154 average time/residue: 2.1268 time to fit residues: 359.4117 Evaluate side-chains 137 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 476 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112805 restraints weight = 27857.967| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.52 r_work: 0.3205 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10229 Z= 0.210 Angle : 0.572 8.330 13913 Z= 0.296 Chirality : 0.038 0.286 1496 Planarity : 0.004 0.033 1662 Dihedral : 15.626 175.937 1748 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.36 % Allowed : 19.57 % Favored : 78.07 % 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: 2.93 (0.24), residues: 1132 helix: 2.65 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 PHE 0.034 0.002 PHE A 605 TYR 0.013 0.002 TYR B 483 ARG 0.005 0.001 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.05214 ( 731) hydrogen bonds : angle 4.15050 ( 2166) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.26172 ( 4) covalent geometry : bond 0.00489 (10227) covalent geometry : angle 0.57122 (13909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8085 (tp40) cc_final: 0.7883 (tp-100) REVERT: A 197 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: A 283 PHE cc_start: 0.8191 (t80) cc_final: 0.7515 (m-80) REVERT: A 394 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8452 (t80) REVERT: B 17 LYS cc_start: 0.8444 (mttt) cc_final: 0.8103 (mmtm) REVERT: B 26 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7279 (mtmm) REVERT: B 71 THR cc_start: 0.7903 (t) cc_final: 0.7553 (m) REVERT: B 318 GLU cc_start: 0.8496 (tt0) cc_final: 0.8101 (tt0) REVERT: B 344 THR cc_start: 0.7893 (t) cc_final: 0.7681 (t) REVERT: B 369 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8548 (mmtt) REVERT: B 590 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7193 (t70) outliers start: 24 outliers final: 13 residues processed: 151 average time/residue: 2.0868 time to fit residues: 345.4559 Evaluate side-chains 139 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 476 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.179070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135875 restraints weight = 27432.262| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.37 r_work: 0.3042 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10229 Z= 0.194 Angle : 0.554 8.671 13913 Z= 0.287 Chirality : 0.037 0.259 1496 Planarity : 0.004 0.033 1662 Dihedral : 15.372 176.588 1748 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 19.96 % Favored : 77.78 % 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: 2.81 (0.24), residues: 1132 helix: 2.55 (0.16), residues: 883 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 PHE 0.031 0.002 PHE A 605 TYR 0.013 0.002 TYR B 496 ARG 0.004 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 731) hydrogen bonds : angle 4.13664 ( 2166) SS BOND : bond 0.00456 ( 2) SS BOND : angle 1.35063 ( 4) covalent geometry : bond 0.00447 (10227) covalent geometry : angle 0.55342 (13909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8655 (tp) REVERT: A 149 GLN cc_start: 0.8334 (tt0) cc_final: 0.7931 (tt0) REVERT: A 193 GLN cc_start: 0.8144 (tp40) cc_final: 0.7903 (tp-100) REVERT: A 197 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: A 283 PHE cc_start: 0.8240 (t80) cc_final: 0.7394 (m-80) REVERT: B 17 LYS cc_start: 0.8557 (mttt) cc_final: 0.8053 (mmtm) REVERT: B 26 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.6954 (mtmm) REVERT: B 71 THR cc_start: 0.7758 (t) cc_final: 0.7436 (m) REVERT: B 318 GLU cc_start: 0.8506 (tt0) cc_final: 0.8123 (tt0) REVERT: B 590 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7097 (t70) outliers start: 23 outliers final: 14 residues processed: 150 average time/residue: 2.0282 time to fit residues: 333.2445 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 248 ASN A 476 HIS B 193 GLN B 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.162329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113113 restraints weight = 27899.441| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.50 r_work: 0.2997 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10229 Z= 0.180 Angle : 0.541 8.886 13913 Z= 0.281 Chirality : 0.036 0.253 1496 Planarity : 0.004 0.035 1662 Dihedral : 14.998 176.983 1748 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 20.55 % Favored : 76.89 % 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: 2.80 (0.24), residues: 1132 helix: 2.54 (0.16), residues: 883 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 514 HIS 0.012 0.001 HIS B 441 PHE 0.032 0.002 PHE A 605 TYR 0.016 0.002 TYR B 496 ARG 0.005 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 731) hydrogen bonds : angle 4.08850 ( 2166) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.37207 ( 4) covalent geometry : bond 0.00412 (10227) covalent geometry : angle 0.54087 (13909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8246 (t80) cc_final: 0.7406 (m-80) REVERT: A 442 LYS cc_start: 0.7731 (mttm) cc_final: 0.7434 (mttm) REVERT: B 17 LYS cc_start: 0.8542 (mttt) cc_final: 0.8039 (mmtm) REVERT: B 26 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6985 (mtmm) REVERT: B 71 THR cc_start: 0.7752 (t) cc_final: 0.7408 (m) REVERT: B 590 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7130 (t70) outliers start: 26 outliers final: 16 residues processed: 149 average time/residue: 1.9915 time to fit residues: 325.8159 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 204 ASN A 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112241 restraints weight = 27893.998| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.51 r_work: 0.3197 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10229 Z= 0.188 Angle : 0.550 8.921 13913 Z= 0.286 Chirality : 0.037 0.250 1496 Planarity : 0.004 0.035 1662 Dihedral : 14.821 177.034 1748 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 20.75 % Favored : 76.99 % 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: 2.75 (0.24), residues: 1132 helix: 2.50 (0.16), residues: 883 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 PHE 0.032 0.002 PHE A 605 TYR 0.015 0.002 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 731) hydrogen bonds : angle 4.10782 ( 2166) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.32930 ( 4) covalent geometry : bond 0.00432 (10227) covalent geometry : angle 0.54924 (13909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8196 (t80) cc_final: 0.7487 (m-80) REVERT: A 442 LYS cc_start: 0.7893 (mttm) cc_final: 0.7660 (mttm) REVERT: B 17 LYS cc_start: 0.8450 (mttt) cc_final: 0.8114 (mmtm) REVERT: B 26 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7204 (mtmm) REVERT: B 576 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: B 590 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7173 (t70) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 2.0488 time to fit residues: 342.9211 Evaluate side-chains 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 204 ASN A 476 HIS B 193 GLN B 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.160826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111438 restraints weight = 28027.038| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.52 r_work: 0.3193 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10229 Z= 0.206 Angle : 0.563 8.886 13913 Z= 0.293 Chirality : 0.037 0.255 1496 Planarity : 0.004 0.036 1662 Dihedral : 14.807 177.258 1748 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.36 % Allowed : 20.85 % Favored : 76.79 % 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: 2.64 (0.24), residues: 1132 helix: 2.43 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 PHE 0.033 0.002 PHE A 605 TYR 0.015 0.002 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 731) hydrogen bonds : angle 4.14934 ( 2166) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.35287 ( 4) covalent geometry : bond 0.00480 (10227) covalent geometry : angle 0.56282 (13909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8269 (tt0) cc_final: 0.7938 (tt0) REVERT: A 283 PHE cc_start: 0.8209 (t80) cc_final: 0.7487 (m-80) REVERT: A 442 LYS cc_start: 0.7888 (mttm) cc_final: 0.7660 (mttm) REVERT: B 17 LYS cc_start: 0.8444 (mttt) cc_final: 0.8052 (mmtm) REVERT: B 71 THR cc_start: 0.7873 (t) cc_final: 0.7549 (m) REVERT: B 417 TYR cc_start: 0.7344 (t80) cc_final: 0.6523 (m-80) REVERT: B 576 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: B 590 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7165 (t70) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 2.0275 time to fit residues: 320.8153 Evaluate side-chains 142 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 204 ASN A 476 HIS B 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130998 restraints weight = 27818.562| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.62 r_work: 0.3190 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10229 Z= 0.138 Angle : 0.518 9.226 13913 Z= 0.271 Chirality : 0.035 0.225 1496 Planarity : 0.004 0.033 1662 Dihedral : 14.477 175.291 1748 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.36 % Allowed : 20.75 % Favored : 76.89 % 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: 2.93 (0.25), residues: 1132 helix: 2.62 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.67 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 PHE 0.028 0.002 PHE A 605 TYR 0.016 0.001 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 731) hydrogen bonds : angle 4.02733 ( 2166) SS BOND : bond 0.00367 ( 2) SS BOND : angle 1.36621 ( 4) covalent geometry : bond 0.00304 (10227) covalent geometry : angle 0.51778 (13909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8219 (t80) cc_final: 0.7465 (m-80) REVERT: A 442 LYS cc_start: 0.7858 (mttm) cc_final: 0.7585 (mttm) REVERT: A 508 MET cc_start: 0.6442 (mmm) cc_final: 0.6210 (tpp) REVERT: B 17 LYS cc_start: 0.8397 (mttt) cc_final: 0.8002 (mmtm) REVERT: B 71 THR cc_start: 0.7755 (t) cc_final: 0.7439 (m) REVERT: B 83 ARG cc_start: 0.7362 (mmm160) cc_final: 0.7115 (tpt90) REVERT: B 417 TYR cc_start: 0.7424 (t80) cc_final: 0.6428 (m-80) REVERT: B 576 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: B 590 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7218 (t70) outliers start: 24 outliers final: 16 residues processed: 146 average time/residue: 1.9933 time to fit residues: 320.2522 Evaluate side-chains 141 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 204 ASN B 193 GLN B 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127434 restraints weight = 27825.109| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.46 r_work: 0.3116 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 10229 Z= 0.214 Angle : 0.854 59.300 13913 Z= 0.500 Chirality : 0.039 0.660 1496 Planarity : 0.004 0.076 1662 Dihedral : 14.477 175.288 1748 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.06 % Allowed : 21.34 % Favored : 76.60 % Cbeta Deviations : 0.09 % 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: 2.92 (0.25), residues: 1132 helix: 2.61 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 175 HIS 0.010 0.001 HIS B 441 PHE 0.143 0.002 PHE A 156 TYR 0.014 0.001 TYR B 496 ARG 0.005 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 731) hydrogen bonds : angle 4.03119 ( 2166) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.34667 ( 4) covalent geometry : bond 0.00485 (10227) covalent geometry : angle 0.85367 (13909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8223 (t80) cc_final: 0.7459 (m-80) REVERT: A 442 LYS cc_start: 0.7848 (mttm) cc_final: 0.7571 (mttm) REVERT: A 508 MET cc_start: 0.6436 (mmm) cc_final: 0.6197 (tpp) REVERT: B 17 LYS cc_start: 0.8422 (mttt) cc_final: 0.7998 (mmtm) REVERT: B 71 THR cc_start: 0.7746 (t) cc_final: 0.7435 (m) REVERT: B 83 ARG cc_start: 0.7346 (mmm160) cc_final: 0.7098 (tpt90) REVERT: B 417 TYR cc_start: 0.7413 (t80) cc_final: 0.6411 (m-80) REVERT: B 576 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: B 590 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7203 (t70) outliers start: 21 outliers final: 15 residues processed: 140 average time/residue: 1.9958 time to fit residues: 307.5408 Evaluate side-chains 138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 204 ASN B 193 GLN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131684 restraints weight = 27903.241| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.45 r_work: 0.3200 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 10229 Z= 0.214 Angle : 0.854 59.300 13913 Z= 0.500 Chirality : 0.039 0.660 1496 Planarity : 0.004 0.076 1662 Dihedral : 14.477 175.288 1748 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.77 % Allowed : 21.53 % Favored : 76.70 % Cbeta Deviations : 0.09 % 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: 2.92 (0.25), residues: 1132 helix: 2.61 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 175 HIS 0.010 0.001 HIS B 441 PHE 0.143 0.002 PHE A 156 TYR 0.014 0.001 TYR B 496 ARG 0.005 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 731) hydrogen bonds : angle 4.03118 ( 2166) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.34667 ( 4) covalent geometry : bond 0.00485 (10227) covalent geometry : angle 0.85367 (13909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12988.68 seconds wall clock time: 220 minutes 39.92 seconds (13239.92 seconds total)