Starting phenix.real_space_refine on Thu Sep 18 19:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvm_47211/09_2025/9dvm_47211_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvm_47211/09_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_47211/09_2025/9dvm_47211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvm_47211/09_2025/9dvm_47211.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvm_47211/09_2025/9dvm_47211_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvm_47211/09_2025/9dvm_47211_trim.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.40, per 1000 atoms: 0.23 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: 2.28 Conformation dependent library (CDL) restraints added in 636.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.41 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: 5.22 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.600 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- 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 : 4.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 604 TYR 0.030 0.001 TYR B 352 PHE 0.013 0.001 PHE B 610 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.000 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00632 (10227) covalent geometry : angle 1.05933 (13909) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.85144 ( 4) hydrogen bonds : bond 0.10775 ( 731) hydrogen bonds : angle 4.79997 ( 2166) *********************** 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 : 0.603 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: 1.3614 time to fit residues: 304.5088 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 : 0.514 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141153 restraints weight = 27643.209| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.43 r_work: 0.3163 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10229 Z= 0.162 Angle : 0.547 7.010 13913 Z= 0.278 Chirality : 0.036 0.228 1496 Planarity : 0.004 0.056 1662 Dihedral : 17.131 176.454 1752 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 21.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.56 (0.25), residues: 1132 helix: 3.19 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.012 0.001 TYR B 483 PHE 0.027 0.002 PHE A 605 TRP 0.011 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00365 (10227) covalent geometry : angle 0.54656 (13909) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.01191 ( 4) hydrogen bonds : bond 0.04718 ( 731) hydrogen bonds : angle 4.15715 ( 2166) *********************** 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 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.570 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: 0.7913 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 197 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: A 204 ASN cc_start: 0.8140 (m-40) cc_final: 0.7682 (m110) REVERT: A 205 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 283 PHE cc_start: 0.8081 (t80) cc_final: 0.7380 (m-80) REVERT: A 417 TYR cc_start: 0.7509 (t80) cc_final: 0.5702 (m-80) REVERT: B 71 THR cc_start: 0.7692 (t) cc_final: 0.7436 (m) REVERT: B 75 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: B 443 TYR cc_start: 0.7691 (m-80) cc_final: 0.7473 (m-80) REVERT: B 590 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6932 (t70) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 1.0869 time to fit residues: 168.8203 Evaluate side-chains 134 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 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 476 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 193 GLN B 306 ASN B 504 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131374 restraints weight = 27561.431| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.49 r_work: 0.3263 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10229 Z= 0.213 Angle : 0.585 8.222 13913 Z= 0.301 Chirality : 0.038 0.308 1496 Planarity : 0.004 0.041 1662 Dihedral : 16.119 173.600 1750 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.75 % Allowed : 18.98 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.25), residues: 1132 helix: 2.69 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.015 0.002 TYR A 352 PHE 0.030 0.002 PHE A 605 TRP 0.013 0.001 TRP A 514 HIS 0.011 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00492 (10227) covalent geometry : angle 0.58523 (13909) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.17505 ( 4) hydrogen bonds : bond 0.05389 ( 731) hydrogen bonds : angle 4.17890 ( 2166) *********************** 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 167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.552 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 149 GLN cc_start: 0.8351 (tt0) cc_final: 0.8022 (tt0) REVERT: A 193 GLN cc_start: 0.8139 (tp40) cc_final: 0.7906 (tp-100) REVERT: A 197 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: A 283 PHE cc_start: 0.8209 (t80) cc_final: 0.7488 (m-80) REVERT: A 394 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8445 (t80) REVERT: B 17 LYS cc_start: 0.8431 (mttt) cc_final: 0.8129 (mmtm) REVERT: B 71 THR cc_start: 0.7836 (t) cc_final: 0.7534 (m) REVERT: B 369 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8550 (mmtt) outliers start: 28 outliers final: 12 residues processed: 161 average time/residue: 1.1480 time to fit residues: 200.4657 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 : 0.526 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115842 restraints weight = 27896.043| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.52 r_work: 0.3350 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3235 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= 0.136 Angle : 0.512 8.908 13913 Z= 0.266 Chirality : 0.035 0.234 1496 Planarity : 0.004 0.032 1662 Dihedral : 15.337 173.458 1748 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.87 % Allowed : 20.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.25), residues: 1132 helix: 2.80 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.011 0.001 TYR B 496 PHE 0.026 0.001 PHE A 605 TRP 0.012 0.001 TRP A 514 HIS 0.010 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00295 (10227) covalent geometry : angle 0.51166 (13909) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.40276 ( 4) hydrogen bonds : bond 0.04586 ( 731) hydrogen bonds : angle 4.03340 ( 2166) *********************** 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 152 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.555 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 140 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 283 PHE cc_start: 0.8169 (t80) cc_final: 0.7467 (m-80) REVERT: B 17 LYS cc_start: 0.8417 (mttt) cc_final: 0.8109 (mmtm) REVERT: B 26 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7239 (mtmm) REVERT: B 71 THR cc_start: 0.7874 (t) cc_final: 0.7539 (m) REVERT: B 369 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8508 (mmtt) REVERT: B 443 TYR cc_start: 0.7723 (m-80) cc_final: 0.7503 (m-80) REVERT: B 590 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7203 (t70) outliers start: 19 outliers final: 12 residues processed: 150 average time/residue: 1.1223 time to fit residues: 183.2248 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 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 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 = 0.3759 r_free = 0.3759 target = 0.162599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.113222 restraints weight = 27896.090| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.52 r_work: 0.3221 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10229 Z= 0.184 Angle : 0.542 8.686 13913 Z= 0.281 Chirality : 0.036 0.265 1496 Planarity : 0.004 0.033 1662 Dihedral : 15.302 176.345 1748 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.46 % Allowed : 20.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.24), residues: 1132 helix: 2.69 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 270 TYR 0.014 0.001 TYR B 496 PHE 0.032 0.002 PHE A 605 TRP 0.013 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00423 (10227) covalent geometry : angle 0.54180 (13909) SS BOND : bond 0.00441 ( 2) SS BOND : angle 1.30905 ( 4) hydrogen bonds : bond 0.04982 ( 731) hydrogen bonds : angle 4.08289 ( 2166) *********************** 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 154 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.540 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: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 283 PHE cc_start: 0.8197 (t80) cc_final: 0.7501 (m-80) REVERT: A 508 MET cc_start: 0.6531 (mmm) cc_final: 0.6314 (tpp) REVERT: B 17 LYS cc_start: 0.8427 (mttt) cc_final: 0.8114 (mmtm) REVERT: B 26 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7268 (mtmm) REVERT: B 71 THR cc_start: 0.7886 (t) cc_final: 0.7541 (m) REVERT: B 304 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 318 GLU cc_start: 0.8514 (tt0) cc_final: 0.8121 (tt0) REVERT: B 590 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7211 (t70) outliers start: 25 outliers final: 14 residues processed: 151 average time/residue: 1.0337 time to fit residues: 170.7749 Evaluate side-chains 145 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 58 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.0040 chunk 76 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.163924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114989 restraints weight = 27670.647| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.52 r_work: 0.3194 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10229 Z= 0.133 Angle : 0.508 9.018 13913 Z= 0.264 Chirality : 0.035 0.235 1496 Planarity : 0.003 0.031 1662 Dihedral : 14.943 175.321 1748 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.25), residues: 1132 helix: 2.78 (0.16), residues: 879 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 83 TYR 0.015 0.001 TYR B 496 PHE 0.027 0.001 PHE A 605 TRP 0.012 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00292 (10227) covalent geometry : angle 0.50718 (13909) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.32396 ( 4) hydrogen bonds : bond 0.04543 ( 731) hydrogen bonds : angle 3.98850 ( 2166) *********************** 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: 21 poor density : 134 time to evaluate : 0.553 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: 0.9078 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 283 PHE cc_start: 0.8187 (t80) cc_final: 0.7514 (m-80) REVERT: A 442 LYS cc_start: 0.7806 (mttm) cc_final: 0.7438 (mmtp) REVERT: A 508 MET cc_start: 0.6548 (mmm) cc_final: 0.6341 (tpp) REVERT: B 17 LYS cc_start: 0.8435 (mttt) cc_final: 0.8118 (mmtm) REVERT: B 26 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7232 (mtmm) REVERT: B 71 THR cc_start: 0.7874 (t) cc_final: 0.7513 (m) REVERT: B 83 ARG cc_start: 0.7394 (mmm160) cc_final: 0.7148 (tpt90) REVERT: B 304 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: B 318 GLU cc_start: 0.8482 (tt0) cc_final: 0.8120 (tt0) REVERT: B 369 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8553 (mmtt) REVERT: B 472 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7356 (mtm110) REVERT: B 590 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7184 (t70) REVERT: B 622 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7976 (mt-10) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 1.1337 time to fit residues: 186.0411 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 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 472 ARG 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 100 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.162041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112747 restraints weight = 27912.843| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.51 r_work: 0.3143 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3620 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= 0.183 Angle : 0.541 8.908 13913 Z= 0.281 Chirality : 0.036 0.255 1496 Planarity : 0.004 0.034 1662 Dihedral : 14.869 177.143 1748 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.46 % Allowed : 20.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.24), residues: 1132 helix: 2.68 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 604 TYR 0.015 0.002 TYR B 496 PHE 0.034 0.002 PHE A 605 TRP 0.014 0.001 TRP A 514 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00422 (10227) covalent geometry : angle 0.54094 (13909) SS BOND : bond 0.00429 ( 2) SS BOND : angle 1.25606 ( 4) hydrogen bonds : bond 0.04962 ( 731) hydrogen bonds : angle 4.04421 ( 2166) *********************** 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 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.518 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: 0.8206 (t80) cc_final: 0.7511 (m-80) REVERT: A 442 LYS cc_start: 0.7842 (mttm) cc_final: 0.7611 (mttm) REVERT: A 508 MET cc_start: 0.6530 (mmm) cc_final: 0.6319 (tpp) REVERT: B 17 LYS cc_start: 0.8440 (mttt) cc_final: 0.8110 (mmtm) REVERT: B 26 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: B 71 THR cc_start: 0.7891 (t) cc_final: 0.7520 (m) REVERT: B 304 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: B 318 GLU cc_start: 0.8540 (tt0) cc_final: 0.8172 (tt0) REVERT: B 443 TYR cc_start: 0.7804 (m-80) cc_final: 0.7581 (m-80) REVERT: B 472 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7398 (mtm110) REVERT: B 576 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: B 590 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7237 (t70) outliers start: 25 outliers final: 16 residues processed: 151 average time/residue: 1.0055 time to fit residues: 166.3182 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 : 0.538 ------------------------------------------------------------------------------- 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 472 ARG 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 23 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.164238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115362 restraints weight = 27894.300| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.51 r_work: 0.3196 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10229 Z= 0.130 Angle : 0.505 9.239 13913 Z= 0.262 Chirality : 0.035 0.226 1496 Planarity : 0.004 0.031 1662 Dihedral : 14.443 175.068 1748 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.17 (0.25), residues: 1132 helix: 2.81 (0.16), residues: 879 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 83 TYR 0.014 0.001 TYR B 496 PHE 0.027 0.001 PHE A 605 TRP 0.013 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00286 (10227) covalent geometry : angle 0.50496 (13909) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.30410 ( 4) hydrogen bonds : bond 0.04485 ( 731) hydrogen bonds : angle 3.94543 ( 2166) *********************** 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 : 0.544 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: 0.8167 (t80) cc_final: 0.7508 (m-80) REVERT: A 442 LYS cc_start: 0.7880 (mttm) cc_final: 0.7497 (mmtp) REVERT: B 17 LYS cc_start: 0.8443 (mttt) cc_final: 0.8113 (mmtm) REVERT: B 83 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7144 (tpt90) REVERT: B 304 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 318 GLU cc_start: 0.8425 (tt0) cc_final: 0.8084 (tt0) REVERT: B 443 TYR cc_start: 0.7779 (m-80) cc_final: 0.7551 (m-80) REVERT: B 472 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7386 (mtm110) REVERT: B 576 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: B 590 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7164 (t70) outliers start: 24 outliers final: 12 residues processed: 149 average time/residue: 1.0518 time to fit residues: 171.4311 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 472 ARG 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 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.161627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112684 restraints weight = 27722.923| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.48 r_work: 0.3000 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3820 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= 0.201 Angle : 0.560 8.965 13913 Z= 0.291 Chirality : 0.037 0.258 1496 Planarity : 0.004 0.035 1662 Dihedral : 14.624 177.331 1748 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.24), residues: 1132 helix: 2.64 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 604 TYR 0.016 0.002 TYR B 496 PHE 0.034 0.002 PHE A 605 TRP 0.015 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00468 (10227) covalent geometry : angle 0.55989 (13909) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.24939 ( 4) hydrogen bonds : bond 0.05077 ( 731) hydrogen bonds : angle 4.06364 ( 2166) *********************** 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 153 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8255 (t80) cc_final: 0.7448 (m-80) REVERT: A 442 LYS cc_start: 0.7803 (mttm) cc_final: 0.7532 (mttm) REVERT: B 17 LYS cc_start: 0.8566 (mttt) cc_final: 0.8010 (mmtm) REVERT: B 26 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.6990 (mtmm) REVERT: B 71 THR cc_start: 0.7736 (t) cc_final: 0.7439 (m) REVERT: B 83 ARG cc_start: 0.7313 (mmm160) cc_final: 0.7090 (tpt90) REVERT: B 304 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: B 318 GLU cc_start: 0.8645 (tt0) cc_final: 0.8267 (tt0) REVERT: B 443 TYR cc_start: 0.7922 (m-80) cc_final: 0.7681 (m-80) REVERT: B 472 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7373 (mtm110) REVERT: B 576 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: B 590 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7131 (t70) REVERT: B 622 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8003 (mt-10) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 1.0121 time to fit residues: 164.2865 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 : 0.520 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 472 ARG 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 85 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 361 ASN B 441 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128575 restraints weight = 27984.254| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.60 r_work: 0.3131 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3920 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= 0.196 Angle : 0.561 8.951 13913 Z= 0.291 Chirality : 0.037 0.248 1496 Planarity : 0.004 0.049 1662 Dihedral : 14.554 176.841 1748 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.26 % Allowed : 21.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.24), residues: 1132 helix: 2.55 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -0.66 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 604 TYR 0.017 0.002 TYR B 496 PHE 0.032 0.002 PHE A 605 TRP 0.022 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00453 (10227) covalent geometry : angle 0.56032 (13909) SS BOND : bond 0.00428 ( 2) SS BOND : angle 1.30289 ( 4) hydrogen bonds : bond 0.05039 ( 731) hydrogen bonds : angle 4.08592 ( 2166) ********************** 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 154 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8221 (t80) cc_final: 0.7474 (m-80) REVERT: A 442 LYS cc_start: 0.7852 (mttm) cc_final: 0.7600 (mttm) REVERT: B 17 LYS cc_start: 0.8423 (mttt) cc_final: 0.8004 (mmtm) REVERT: B 71 THR cc_start: 0.7779 (t) cc_final: 0.7476 (m) REVERT: B 83 ARG cc_start: 0.7349 (mmm160) cc_final: 0.7127 (tpt90) REVERT: B 304 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 417 TYR cc_start: 0.7369 (t80) cc_final: 0.6446 (m-80) REVERT: B 443 TYR cc_start: 0.7920 (m-80) cc_final: 0.7670 (m-80) REVERT: B 472 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7441 (mtm110) REVERT: B 538 ASP cc_start: 0.7650 (t0) cc_final: 0.7361 (t0) REVERT: B 576 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: B 590 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7237 (t70) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 0.8900 time to fit residues: 145.2038 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 : 0.512 ------------------------------------------------------------------------------- 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 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 402 SER Chi-restraints excluded: chain B residue 472 ARG 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 73 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 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 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 = 0.3862 r_free = 0.3862 target = 0.168908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126437 restraints weight = 27918.497| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.57 r_work: 0.3161 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3969 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= 0.185 Angle : 0.554 9.030 13913 Z= 0.288 Chirality : 0.037 0.245 1496 Planarity : 0.004 0.061 1662 Dihedral : 14.489 176.749 1748 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 21.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.24), residues: 1132 helix: 2.53 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -0.64 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 604 TYR 0.016 0.002 TYR B 496 PHE 0.032 0.002 PHE A 605 TRP 0.021 0.001 TRP B 175 HIS 0.011 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00426 (10227) covalent geometry : angle 0.55339 (13909) SS BOND : bond 0.00424 ( 2) SS BOND : angle 1.33075 ( 4) hydrogen bonds : bond 0.04986 ( 731) hydrogen bonds : angle 4.07643 ( 2166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.84 seconds wall clock time: 108 minutes 17.21 seconds (6497.21 seconds total)