Starting phenix.real_space_refine on Tue May 20 08:07:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvm_47211/05_2025/9dvm_47211_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvm_47211/05_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_47211/05_2025/9dvm_47211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvm_47211/05_2025/9dvm_47211.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvm_47211/05_2025/9dvm_47211_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvm_47211/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.50, per 1000 atoms: 0.49 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: 4.86 Conformation dependent library (CDL) restraints added in 1.3 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: 1.15 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: 6.76 Time building geometry restraints manager: 5.87 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: 3.650 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: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.210 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.350 ------------------------------------------------------------------------------- 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 : 1.480 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: 2.4372 time to fit residues: 548.9261 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 : 1.258 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.143112 restraints weight = 27596.406| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.47 r_work: 0.3239 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.98840 ( 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 : 1.450 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: 0.7963 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 197 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: A 283 PHE cc_start: 0.8108 (t80) cc_final: 0.7486 (m-80) REVERT: A 417 TYR cc_start: 0.7544 (t80) cc_final: 0.5770 (m-80) REVERT: B 71 THR cc_start: 0.7773 (t) cc_final: 0.7502 (m) REVERT: B 318 GLU cc_start: 0.8541 (tt0) cc_final: 0.8314 (tt0) REVERT: B 590 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6985 (t70) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 2.0684 time to fit residues: 328.1134 Evaluate side-chains 134 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 127 ASN B 193 GLN B 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138567 restraints weight = 27321.379| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.45 r_work: 0.3054 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10229 Z= 0.187 Angle : 0.546 8.267 13913 Z= 0.281 Chirality : 0.037 0.270 1496 Planarity : 0.004 0.040 1662 Dihedral : 16.134 172.858 1750 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 20.35 % Favored : 77.48 % 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: 3.20 (0.25), residues: 1132 helix: 2.87 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.84 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 PHE 0.027 0.002 PHE A 605 TYR 0.013 0.001 TYR A 352 ARG 0.005 0.001 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 731) hydrogen bonds : angle 4.11162 ( 2166) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.22668 ( 4) covalent geometry : bond 0.00427 (10227) covalent geometry : angle 0.54520 (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 159 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 193 GLN cc_start: 0.8133 (tp40) cc_final: 0.7888 (tp-100) REVERT: A 197 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: A 283 PHE cc_start: 0.8188 (t80) cc_final: 0.7472 (m-80) REVERT: B 71 THR cc_start: 0.7758 (t) cc_final: 0.7452 (m) REVERT: B 369 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8446 (mmtt) REVERT: B 590 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7025 (t70) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 2.0308 time to fit residues: 345.1081 Evaluate side-chains 138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 A residue 631 VAL 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: 3.9990 chunk 87 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.176790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131859 restraints weight = 27367.764| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.42 r_work: 0.2961 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10229 Z= 0.206 Angle : 0.562 8.388 13913 Z= 0.291 Chirality : 0.037 0.274 1496 Planarity : 0.004 0.033 1662 Dihedral : 15.710 175.855 1748 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.97 % 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: 2.90 (0.24), residues: 1132 helix: 2.65 (0.16), residues: 879 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 253 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 0.012 0.002 TYR B 496 ARG 0.004 0.001 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.05152 ( 731) hydrogen bonds : angle 4.16537 ( 2166) SS BOND : bond 0.00506 ( 2) SS BOND : angle 1.39536 ( 4) covalent geometry : bond 0.00480 (10227) covalent geometry : angle 0.56151 (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 161 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.338 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: 0.8218 (t80) cc_final: 0.7392 (m-80) REVERT: B 17 LYS cc_start: 0.8554 (mttt) cc_final: 0.8074 (mmtm) REVERT: B 26 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7017 (mtmm) REVERT: B 71 THR cc_start: 0.7740 (t) cc_final: 0.7428 (m) REVERT: B 304 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 318 GLU cc_start: 0.8662 (tt0) cc_final: 0.8287 (tt0) REVERT: B 369 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8459 (mmtt) REVERT: B 590 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7101 (t70) outliers start: 27 outliers final: 15 residues processed: 157 average time/residue: 2.0077 time to fit residues: 345.3363 Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 304 GLU 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 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: 0.8980 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 104 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 193 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.163293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114072 restraints weight = 27846.984| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.51 r_work: 0.3200 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10229 Z= 0.158 Angle : 0.528 8.832 13913 Z= 0.274 Chirality : 0.036 0.246 1496 Planarity : 0.004 0.033 1662 Dihedral : 15.297 175.593 1748 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 20.55 % 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: 2.99 (0.24), residues: 1132 helix: 2.71 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 255 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 0.029 0.002 PHE A 605 TYR 0.013 0.001 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 731) hydrogen bonds : angle 4.07218 ( 2166) SS BOND : bond 0.00418 ( 2) SS BOND : angle 1.34461 ( 4) covalent geometry : bond 0.00356 (10227) covalent geometry : angle 0.52787 (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 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.351 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: 0.9086 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 204 ASN cc_start: 0.7935 (m-40) cc_final: 0.7567 (m110) REVERT: A 205 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 283 PHE cc_start: 0.8215 (t80) cc_final: 0.7519 (m-80) REVERT: B 17 LYS cc_start: 0.8443 (mttt) cc_final: 0.8112 (mmtm) REVERT: B 26 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7248 (mtmm) REVERT: B 71 THR cc_start: 0.7885 (t) cc_final: 0.7533 (m) REVERT: B 304 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: B 318 GLU cc_start: 0.8456 (tt0) cc_final: 0.8067 (tt0) REVERT: B 590 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7207 (t70) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 1.9311 time to fit residues: 316.2907 Evaluate side-chains 148 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 218 LEU 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 B residue 26 LYS Chi-restraints excluded: chain B residue 304 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 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: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 476 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 504 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.161706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112251 restraints weight = 27902.025| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.52 r_work: 0.3197 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10229 Z= 0.209 Angle : 0.562 8.729 13913 Z= 0.291 Chirality : 0.037 0.268 1496 Planarity : 0.004 0.035 1662 Dihedral : 15.181 177.866 1748 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 2.76 (0.24), residues: 1132 helix: 2.53 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.012 0.001 HIS B 441 PHE 0.033 0.002 PHE A 605 TYR 0.014 0.002 TYR B 496 ARG 0.004 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 731) hydrogen bonds : angle 4.14523 ( 2166) SS BOND : bond 0.00457 ( 2) SS BOND : angle 1.34257 ( 4) covalent geometry : bond 0.00487 (10227) covalent geometry : angle 0.56175 (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 157 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8203 (t80) cc_final: 0.7485 (m-80) REVERT: A 442 LYS cc_start: 0.7805 (mttm) cc_final: 0.7576 (mttm) REVERT: B 17 LYS cc_start: 0.8428 (mttt) cc_final: 0.8095 (mmtm) REVERT: B 26 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7265 (mtmm) REVERT: B 71 THR cc_start: 0.7898 (t) cc_final: 0.7526 (m) REVERT: B 304 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: B 318 GLU cc_start: 0.8474 (tt0) cc_final: 0.8077 (tt0) REVERT: B 576 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: B 590 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7182 (t70) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 1.9906 time to fit residues: 335.4886 Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 304 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.164058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115581 restraints weight = 27943.171| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.50 r_work: 0.3218 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10229 Z= 0.164 Angle : 0.531 9.070 13913 Z= 0.276 Chirality : 0.036 0.239 1496 Planarity : 0.004 0.035 1662 Dihedral : 14.788 176.193 1748 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 21.04 % 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: 2.86 (0.24), residues: 1132 helix: 2.60 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 255 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 0.030 0.002 PHE A 605 TYR 0.015 0.001 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 731) hydrogen bonds : angle 4.06386 ( 2166) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.36540 ( 4) covalent geometry : bond 0.00371 (10227) covalent geometry : angle 0.53047 (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 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8185 (t80) cc_final: 0.7476 (m-80) REVERT: A 442 LYS cc_start: 0.7892 (mttm) cc_final: 0.7656 (mttm) REVERT: B 17 LYS cc_start: 0.8425 (mttt) cc_final: 0.8106 (mmtm) REVERT: B 26 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7217 (mtmm) REVERT: B 304 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 417 TYR cc_start: 0.7248 (t80) cc_final: 0.6555 (m-80) REVERT: B 576 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: B 590 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7178 (t70) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 2.0094 time to fit residues: 327.7470 Evaluate side-chains 145 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 304 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115272 restraints weight = 28022.561| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.50 r_work: 0.3007 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3771 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= 0.167 Angle : 0.531 9.016 13913 Z= 0.277 Chirality : 0.036 0.244 1496 Planarity : 0.004 0.034 1662 Dihedral : 14.664 176.546 1748 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 2.89 (0.24), residues: 1132 helix: 2.62 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 255 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 0.032 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 0.04853 ( 731) hydrogen bonds : angle 4.05434 ( 2166) SS BOND : bond 0.00411 ( 2) SS BOND : angle 1.31833 ( 4) covalent geometry : bond 0.00382 (10227) covalent geometry : angle 0.53083 (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 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8247 (t80) cc_final: 0.7411 (m-80) REVERT: A 442 LYS cc_start: 0.7804 (mttm) cc_final: 0.7528 (mttm) REVERT: B 17 LYS cc_start: 0.8554 (mttt) cc_final: 0.8042 (mmtm) REVERT: B 26 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6955 (mtmm) REVERT: B 71 THR cc_start: 0.7719 (t) cc_final: 0.7427 (m) REVERT: B 83 ARG cc_start: 0.7266 (mmm160) cc_final: 0.7039 (tpt90) REVERT: B 304 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: B 417 TYR cc_start: 0.7295 (t80) cc_final: 0.6414 (m-80) REVERT: B 576 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: B 590 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7145 (t70) outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 2.0015 time to fit residues: 329.0770 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 304 GLU 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 549 GLU 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: 1.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.173669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132415 restraints weight = 27681.808| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.42 r_work: 0.3137 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3777 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= 0.144 Angle : 0.521 9.202 13913 Z= 0.272 Chirality : 0.035 0.232 1496 Planarity : 0.004 0.032 1662 Dihedral : 14.479 175.605 1748 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 2.99 (0.24), residues: 1132 helix: 2.70 (0.16), residues: 878 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 PHE 0.029 0.002 PHE A 605 TYR 0.017 0.001 TYR B 496 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 731) hydrogen bonds : angle 4.00684 ( 2166) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.35101 ( 4) covalent geometry : bond 0.00321 (10227) covalent geometry : angle 0.52058 (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 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8202 (t80) cc_final: 0.7433 (m-80) REVERT: A 442 LYS cc_start: 0.7857 (mttm) cc_final: 0.7596 (mttm) REVERT: A 508 MET cc_start: 0.6436 (mmm) cc_final: 0.6172 (tpp) REVERT: B 17 LYS cc_start: 0.8444 (mttt) cc_final: 0.8063 (mmtm) REVERT: B 71 THR cc_start: 0.7785 (t) cc_final: 0.7479 (m) REVERT: B 83 ARG cc_start: 0.7320 (mmm160) cc_final: 0.7081 (tpt90) REVERT: B 304 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: B 417 TYR cc_start: 0.7321 (t80) cc_final: 0.6449 (m-80) REVERT: B 576 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: B 590 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7113 (t70) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 2.0047 time to fit residues: 320.9492 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 304 GLU 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: 7.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 69 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 B 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.177220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132949 restraints weight = 27549.261| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.40 r_work: 0.3233 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10229 Z= 0.136 Angle : 0.515 9.264 13913 Z= 0.268 Chirality : 0.035 0.231 1496 Planarity : 0.004 0.067 1662 Dihedral : 14.317 175.602 1748 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 21.14 % 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: 3.07 (0.24), residues: 1132 helix: 2.75 (0.16), residues: 878 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 254 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 0.030 0.002 PHE A 605 TYR 0.017 0.001 TYR B 496 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 731) hydrogen bonds : angle 3.97075 ( 2166) SS BOND : bond 0.00380 ( 2) SS BOND : angle 1.34122 ( 4) covalent geometry : bond 0.00300 (10227) covalent geometry : angle 0.51430 (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 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8197 (t80) cc_final: 0.7462 (m-80) REVERT: A 442 LYS cc_start: 0.7864 (mttm) cc_final: 0.7600 (mttm) REVERT: A 508 MET cc_start: 0.6428 (mmm) cc_final: 0.6172 (tpp) REVERT: B 17 LYS cc_start: 0.8437 (mttt) cc_final: 0.8060 (mmtm) REVERT: B 71 THR cc_start: 0.7811 (t) cc_final: 0.7482 (m) REVERT: B 83 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7124 (tpt90) REVERT: B 304 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 417 TYR cc_start: 0.7365 (t80) cc_final: 0.6455 (m-80) REVERT: B 576 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: B 590 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7159 (t70) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 1.9873 time to fit residues: 318.0182 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 : 1.460 ------------------------------------------------------------------------------- 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 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 304 GLU 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 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: 0.8980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.177099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133979 restraints weight = 27641.803| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.52 r_work: 0.3142 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10229 Z= 0.139 Angle : 0.518 9.291 13913 Z= 0.270 Chirality : 0.035 0.234 1496 Planarity : 0.004 0.045 1662 Dihedral : 14.215 175.662 1748 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.97 % Allowed : 21.44 % 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: 3.09 (0.24), residues: 1132 helix: 2.76 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.64 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 PHE 0.029 0.001 PHE A 605 TYR 0.016 0.001 TYR B 496 ARG 0.007 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 731) hydrogen bonds : angle 3.95761 ( 2166) SS BOND : bond 0.00380 ( 2) SS BOND : angle 1.34959 ( 4) covalent geometry : bond 0.00310 (10227) covalent geometry : angle 0.51736 (13909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12436.31 seconds wall clock time: 213 minutes 11.80 seconds (12791.80 seconds total)