Starting phenix.real_space_refine on Thu Sep 18 19:56:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvo_47213/09_2025/9dvo_47213_trim.cif" } resolution = 3.1 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= 0.009 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 38 5.49 5 S 42 5.16 5 C 6508 2.51 5 N 1583 2.21 5 O 1772 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 3 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: 19515 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: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 173 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 3.08, per 1000 atoms: 0.16 Number of scatterers: 19515 At special positions: 0 Unit cell: (107.3, 93.525, 123.25, 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 38 15.00 O 1772 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: 1.87 Conformation dependent library (CDL) restraints added in 492.7 milliseconds Enol-peptide restraints added in 715.3 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 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.431A 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 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.368A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.868A 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 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.063A 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: 3.746A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.542A 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: 3.821A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 622 Proline residue: A 598 - end of helix removed outlier: 3.651A pdb=" N GLU A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.468A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 47 through 98 Processing helix chain 'B' and resid 123 through 168 Processing helix chain 'B' and resid 171 through 179 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: 3.695A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.122A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 267 through 295 removed outlier: 5.394A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.984A 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: 3.645A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.516A pdb=" N TRP B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.070A 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 500 removed outlier: 4.145A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.118A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.790A 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 735 hydrogen bonds defined for protein. 2172 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: 4.97 Time building geometry restraints manager: 2.39 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: 27 1.23 - 1.42: 4397 1.42 - 1.62: 5732 1.62 - 1.81: 83 Bond restraints: 19791 Sorted by residual: bond pdb=" O45 I8P B 702 " pdb=" PB5 I8P B 702 " ideal model delta sigma weight residual 1.695 1.582 0.113 2.00e-02 2.50e+03 3.18e+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 3.08e+01 bond pdb=" O45 I8P B 703 " pdb=" PB5 I8P B 703 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O45 I8P A 704 " pdb=" PB5 I8P A 704 " ideal model delta sigma weight residual 1.695 1.585 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" O3P CPL A 707 " pdb=" P CPL A 707 " ideal model delta sigma weight residual 1.633 1.739 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 19786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 35259 3.05 - 6.09: 161 6.09 - 9.14: 74 9.14 - 12.19: 21 12.19 - 15.23: 18 Bond angle restraints: 35533 Sorted by residual: angle pdb=" O1P CPL A 707 " pdb=" P CPL A 707 " pdb=" O2P CPL A 707 " ideal model delta sigma weight residual 119.55 134.78 -15.23 3.00e+00 1.11e-01 2.58e+01 angle pdb=" O1P CPL B 705 " pdb=" P CPL B 705 " pdb=" O2P CPL B 705 " ideal model delta sigma weight residual 119.55 134.77 -15.22 3.00e+00 1.11e-01 2.57e+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 99.81 14.04 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 99.83 14.02 3.00e+00 1.11e-01 2.18e+01 angle pdb=" O65 I8P B 703 " pdb=" PB5 I8P B 703 " pdb=" O75 I8P B 703 " ideal model delta sigma weight residual 113.85 99.87 13.98 3.00e+00 1.11e-01 2.17e+01 ... (remaining 35528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 9223 35.74 - 71.48: 373 71.48 - 107.22: 24 107.22 - 142.96: 8 142.96 - 178.70: 7 Dihedral angle restraints: 9635 sinusoidal: 5203 harmonic: 4432 Sorted by residual: dihedral pdb=" O15 I8P A 705 " pdb=" O45 I8P A 705 " pdb=" PA5 I8P A 705 " pdb=" PB5 I8P A 705 " ideal model delta sinusoidal sigma weight residual 236.14 57.44 178.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O35 I8P A 705 " pdb=" O45 I8P A 705 " pdb=" PA5 I8P A 705 " pdb=" PB5 I8P A 705 " ideal model delta sinusoidal sigma weight residual 349.23 171.47 177.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O25 I8P B 703 " pdb=" O45 I8P B 703 " pdb=" PA5 I8P B 703 " pdb=" PB5 I8P B 703 " ideal model delta sinusoidal sigma weight residual 121.17 -63.87 -174.96 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: 1350 0.071 - 0.142: 124 0.142 - 0.213: 12 0.213 - 0.284: 2 0.284 - 0.355: 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 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C17 CLR B 704 " pdb=" C13 CLR B 704 " pdb=" C16 CLR B 704 " pdb=" C20 CLR B 704 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C13 CLR B 704 " pdb=" C12 CLR B 704 " pdb=" C14 CLR B 704 " pdb=" C17 CLR B 704 " both_signs ideal model delta sigma weight residual False -2.93 -3.26 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1493 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 544 " 0.094 2.00e-02 2.50e+03 9.84e-02 1.45e+02 pdb=" CG ASN B 544 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 544 " -0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN B 544 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 544 " 0.148 2.00e-02 2.50e+03 pdb="HD22 ASN B 544 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 479 " -0.048 2.00e-02 2.50e+03 4.98e-02 3.72e+01 pdb=" CG ASN A 479 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 479 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 479 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 479 " -0.074 2.00e-02 2.50e+03 pdb="HD22 ASN A 479 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 504 " -0.013 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" N SER A 505 " 0.042 2.00e-02 2.50e+03 pdb=" CA SER A 505 " -0.011 2.00e-02 2.50e+03 pdb=" H SER A 505 " -0.018 2.00e-02 2.50e+03 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 198 2.05 - 2.69: 29235 2.69 - 3.32: 59276 3.32 - 3.96: 73588 3.96 - 4.60: 115429 Nonbonded interactions: 277726 Sorted by model distance: nonbonded pdb=" HG LEU A 7 " pdb="HD11 ILE A 11 " model vdw 1.409 2.440 nonbonded pdb=" O LEU A 7 " pdb="HG13 ILE A 11 " model vdw 1.612 2.620 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.613 2.450 nonbonded pdb="HH12 ARG A 270 " pdb=" O2 PO4 A 703 " model vdw 1.623 2.450 nonbonded pdb=" HG SER A 402 " pdb=" OE2 GLU A 600 " model vdw 1.643 2.450 ... (remaining 277721 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 703 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 705)) } 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: 5.130 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.920 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.113 10221 Z= 0.319 Angle : 1.064 15.233 13901 Z= 0.431 Chirality : 0.046 0.355 1496 Planarity : 0.003 0.031 1662 Dihedral : 20.325 178.698 3989 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.79 % Allowed : 19.27 % Favored : 79.94 % 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: 3.39 (0.25), residues: 1132 helix: 3.20 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 157 TYR 0.024 0.001 TYR A 483 PHE 0.015 0.001 PHE A 487 TRP 0.008 0.001 TRP B 528 HIS 0.004 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00610 (10219) covalent geometry : angle 1.06417 (13897) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.53129 ( 4) hydrogen bonds : bond 0.11440 ( 735) hydrogen bonds : angle 4.61762 ( 2172) *********************** 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 173 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7450 (mtpt) cc_final: 0.7081 (mtmm) REVERT: A 77 LEU cc_start: 0.8797 (tm) cc_final: 0.8595 (tp) REVERT: A 193 GLN cc_start: 0.7491 (pp30) cc_final: 0.7210 (pp30) REVERT: A 213 LYS cc_start: 0.7543 (mmtp) cc_final: 0.7010 (mmtp) REVERT: A 417 TYR cc_start: 0.7527 (t80) cc_final: 0.7285 (t80) REVERT: A 472 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6924 (tpt170) REVERT: A 508 MET cc_start: 0.6332 (mmt) cc_final: 0.5959 (tpp) REVERT: B 357 PHE cc_start: 0.7303 (t80) cc_final: 0.7027 (t80) REVERT: B 508 MET cc_start: 0.6343 (mmt) cc_final: 0.5455 (mmm) outliers start: 8 outliers final: 6 residues processed: 173 average time/residue: 0.2977 time to fit residues: 68.1515 Evaluate side-chains 131 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN B 441 HIS B 452 GLN B 616 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.172367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130874 restraints weight = 29417.525| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.51 r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10221 Z= 0.205 Angle : 0.561 6.069 13901 Z= 0.294 Chirality : 0.037 0.203 1496 Planarity : 0.004 0.030 1662 Dihedral : 18.686 169.978 1756 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 17.11 % Favored : 80.53 % 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 (0.25), residues: 1132 helix: 2.85 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.016 0.002 TYR A 483 PHE 0.036 0.002 PHE A 605 TRP 0.017 0.002 TRP B 528 HIS 0.008 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00460 (10219) covalent geometry : angle 0.56136 (13897) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.63501 ( 4) hydrogen bonds : bond 0.05225 ( 735) hydrogen bonds : angle 4.29143 ( 2172) *********************** 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 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7772 (mttp) REVERT: A 472 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6785 (tpt90) REVERT: A 508 MET cc_start: 0.6438 (mmt) cc_final: 0.5991 (tpp) REVERT: A 608 ASN cc_start: 0.8715 (m-40) cc_final: 0.8409 (m-40) REVERT: B 199 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: B 445 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7347 (p90) REVERT: B 508 MET cc_start: 0.6547 (mmt) cc_final: 0.5607 (mmm) outliers start: 24 outliers final: 13 residues processed: 143 average time/residue: 0.3154 time to fit residues: 59.0343 Evaluate side-chains 136 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE 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 584 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.170001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127961 restraints weight = 29515.115| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.50 r_work: 0.3198 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10221 Z= 0.181 Angle : 0.527 7.409 13901 Z= 0.276 Chirality : 0.036 0.258 1496 Planarity : 0.004 0.033 1662 Dihedral : 17.675 161.280 1750 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 16.62 % Favored : 80.83 % 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: 2.84 (0.25), residues: 1132 helix: 2.76 (0.16), residues: 879 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.015 0.001 TYR A 483 PHE 0.031 0.002 PHE A 605 TRP 0.017 0.001 TRP B 528 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00408 (10219) covalent geometry : angle 0.52732 (13897) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.42969 ( 4) hydrogen bonds : bond 0.05049 ( 735) hydrogen bonds : angle 4.14769 ( 2172) *********************** 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 145 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8051 (mttp) REVERT: A 59 PHE cc_start: 0.6832 (m-10) cc_final: 0.6333 (m-80) REVERT: A 472 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6756 (tpt170) REVERT: A 508 MET cc_start: 0.6387 (mmt) cc_final: 0.5907 (tpp) REVERT: B 199 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: B 508 MET cc_start: 0.6588 (mmt) cc_final: 0.6164 (mmm) outliers start: 26 outliers final: 15 residues processed: 141 average time/residue: 0.2789 time to fit residues: 52.2646 Evaluate side-chains 130 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.168523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126882 restraints weight = 29383.290| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.49 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10221 Z= 0.181 Angle : 0.524 8.067 13901 Z= 0.277 Chirality : 0.036 0.254 1496 Planarity : 0.004 0.033 1662 Dihedral : 17.090 150.384 1748 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.75 % Allowed : 16.03 % Favored : 81.22 % 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: 2.75 (0.24), residues: 1132 helix: 2.70 (0.16), residues: 880 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.014 0.001 TYR A 483 PHE 0.033 0.002 PHE A 605 TRP 0.010 0.001 TRP A 514 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00408 (10219) covalent geometry : angle 0.52447 (13897) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.52852 ( 4) hydrogen bonds : bond 0.04955 ( 735) hydrogen bonds : angle 4.10477 ( 2172) *********************** 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 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8060 (mttp) REVERT: A 59 PHE cc_start: 0.7013 (m-10) cc_final: 0.6568 (m-80) REVERT: A 83 ARG cc_start: 0.8121 (tpt-90) cc_final: 0.7810 (tpt170) REVERT: A 472 ARG cc_start: 0.7413 (mtp180) cc_final: 0.6760 (tpt170) REVERT: A 508 MET cc_start: 0.6393 (mmt) cc_final: 0.5974 (tpp) REVERT: B 199 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: B 318 GLU cc_start: 0.8716 (tt0) cc_final: 0.8446 (tt0) REVERT: B 508 MET cc_start: 0.6598 (mmt) cc_final: 0.6195 (mmm) outliers start: 28 outliers final: 23 residues processed: 138 average time/residue: 0.2948 time to fit residues: 54.2972 Evaluate side-chains 136 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 60 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129211 restraints weight = 29355.918| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.50 r_work: 0.3212 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10221 Z= 0.120 Angle : 0.479 8.626 13901 Z= 0.252 Chirality : 0.034 0.215 1496 Planarity : 0.003 0.031 1662 Dihedral : 16.375 143.362 1748 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.26 % Allowed : 16.52 % Favored : 81.22 % 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: 3.01 (0.25), residues: 1132 helix: 2.88 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.011 0.001 TYR A 272 PHE 0.026 0.001 PHE A 605 TRP 0.010 0.001 TRP B 528 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00253 (10219) covalent geometry : angle 0.47846 (13897) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.63520 ( 4) hydrogen bonds : bond 0.04462 ( 735) hydrogen bonds : angle 3.96490 ( 2172) *********************** 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 138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7973 (mttp) REVERT: A 59 PHE cc_start: 0.6901 (m-10) cc_final: 0.6482 (m-80) REVERT: A 83 ARG cc_start: 0.8059 (tpt-90) cc_final: 0.7728 (tpt170) REVERT: A 472 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6680 (tpt170) REVERT: A 508 MET cc_start: 0.6182 (mmt) cc_final: 0.5779 (tpp) REVERT: B 128 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 199 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: B 273 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7935 (ptp90) REVERT: B 508 MET cc_start: 0.6548 (mmt) cc_final: 0.6155 (mmm) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.2854 time to fit residues: 51.6116 Evaluate side-chains 133 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN B 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.166949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126056 restraints weight = 29363.663| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.54 r_work: 0.3143 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10221 Z= 0.185 Angle : 0.522 8.239 13901 Z= 0.276 Chirality : 0.036 0.251 1496 Planarity : 0.004 0.040 1662 Dihedral : 16.220 141.935 1748 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.36 % Allowed : 16.72 % Favored : 80.92 % 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: 2.72 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 548 TYR 0.013 0.002 TYR A 483 PHE 0.034 0.002 PHE A 605 TRP 0.010 0.001 TRP A 514 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00420 (10219) covalent geometry : angle 0.52197 (13897) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.51764 ( 4) hydrogen bonds : bond 0.04910 ( 735) hydrogen bonds : angle 4.05118 ( 2172) *********************** 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 138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8024 (mttp) REVERT: A 83 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7734 (tpt170) REVERT: A 258 LYS cc_start: 0.5558 (mmmt) cc_final: 0.5283 (mttm) REVERT: A 472 ARG cc_start: 0.7367 (mtp180) cc_final: 0.6697 (tpt170) REVERT: A 508 MET cc_start: 0.6237 (mmt) cc_final: 0.5881 (tpp) REVERT: B 128 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7545 (tt) REVERT: B 199 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: B 273 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7973 (ptp90) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.2651 time to fit residues: 47.2612 Evaluate side-chains 132 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.173592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132904 restraints weight = 29099.518| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.52 r_work: 0.3192 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10221 Z= 0.138 Angle : 0.490 8.693 13901 Z= 0.258 Chirality : 0.034 0.220 1496 Planarity : 0.003 0.039 1662 Dihedral : 15.476 142.040 1748 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.36 % Allowed : 17.11 % Favored : 80.53 % 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: 2.92 (0.24), residues: 1132 helix: 2.83 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.011 0.001 TYR A 367 PHE 0.028 0.001 PHE A 605 TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00299 (10219) covalent geometry : angle 0.49035 (13897) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.62507 ( 4) hydrogen bonds : bond 0.04570 ( 735) hydrogen bonds : angle 3.96585 ( 2172) *********************** 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 133 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7784 (tpt170) REVERT: A 258 LYS cc_start: 0.5589 (mmmt) cc_final: 0.5302 (mttm) REVERT: A 472 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6703 (tpt170) REVERT: A 508 MET cc_start: 0.6264 (mmt) cc_final: 0.5931 (tpp) REVERT: A 577 ILE cc_start: 0.7461 (tt) cc_final: 0.7156 (pt) REVERT: B 199 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: B 273 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7977 (ptp90) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 0.2603 time to fit residues: 45.7500 Evaluate side-chains 127 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.176248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.137631 restraints weight = 28929.036| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.36 r_work: 0.3254 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10221 Z= 0.135 Angle : 0.488 8.709 13901 Z= 0.257 Chirality : 0.034 0.228 1496 Planarity : 0.003 0.042 1662 Dihedral : 15.179 140.814 1748 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 16.72 % Favored : 80.83 % 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: 2.98 (0.24), residues: 1132 helix: 2.86 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.013 0.001 TYR A 367 PHE 0.028 0.001 PHE A 605 TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00292 (10219) covalent geometry : angle 0.48839 (13897) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.56195 ( 4) hydrogen bonds : bond 0.04510 ( 735) hydrogen bonds : angle 3.93208 ( 2172) *********************** 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 135 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7747 (tpt170) REVERT: A 186 TYR cc_start: 0.7373 (t80) cc_final: 0.7149 (t80) REVERT: A 258 LYS cc_start: 0.5615 (mmmt) cc_final: 0.5316 (mttm) REVERT: A 472 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6747 (tpt170) REVERT: A 508 MET cc_start: 0.6236 (mmt) cc_final: 0.5937 (tpp) REVERT: A 577 ILE cc_start: 0.7476 (tt) cc_final: 0.7237 (pt) REVERT: B 199 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: B 213 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8305 (mtpp) REVERT: B 273 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7953 (ptp90) REVERT: B 309 SER cc_start: 0.9109 (t) cc_final: 0.8824 (p) outliers start: 25 outliers final: 21 residues processed: 133 average time/residue: 0.2497 time to fit residues: 45.0131 Evaluate side-chains 132 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123615 restraints weight = 29258.753| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.48 r_work: 0.3138 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10221 Z= 0.207 Angle : 0.540 8.438 13901 Z= 0.285 Chirality : 0.037 0.273 1496 Planarity : 0.004 0.045 1662 Dihedral : 15.389 149.296 1748 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.65 % Allowed : 16.13 % Favored : 81.22 % 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: 2.71 (0.24), residues: 1132 helix: 2.65 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 82 TYR 0.014 0.002 TYR A 483 PHE 0.035 0.002 PHE A 605 TRP 0.011 0.001 TRP A 514 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00474 (10219) covalent geometry : angle 0.53984 (13897) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.46363 ( 4) hydrogen bonds : bond 0.05037 ( 735) hydrogen bonds : angle 4.07521 ( 2172) *********************** 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 140 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8003 (tpt-90) cc_final: 0.7691 (tpt170) REVERT: A 258 LYS cc_start: 0.5605 (mmmt) cc_final: 0.5343 (mttm) REVERT: A 472 ARG cc_start: 0.7367 (mtp180) cc_final: 0.6673 (tpt170) REVERT: B 199 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6870 (mt-10) REVERT: B 213 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8195 (mtpp) REVERT: B 273 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7965 (ptp90) REVERT: B 318 GLU cc_start: 0.8744 (tt0) cc_final: 0.8367 (tt0) outliers start: 27 outliers final: 24 residues processed: 136 average time/residue: 0.2662 time to fit residues: 48.1369 Evaluate side-chains 137 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.174839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.139556 restraints weight = 28949.003| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.22 r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10221 Z= 0.127 Angle : 0.494 8.830 13901 Z= 0.259 Chirality : 0.034 0.225 1496 Planarity : 0.003 0.044 1662 Dihedral : 15.111 144.252 1748 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 16.62 % Favored : 81.12 % 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: 2.92 (0.24), residues: 1132 helix: 2.82 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.017 0.001 TYR A 367 PHE 0.027 0.001 PHE A 605 TRP 0.010 0.001 TRP A 514 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00270 (10219) covalent geometry : angle 0.49361 (13897) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.64600 ( 4) hydrogen bonds : bond 0.04539 ( 735) hydrogen bonds : angle 3.95130 ( 2172) ********************** 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 131 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8047 (tpt-90) cc_final: 0.7753 (tpt170) REVERT: A 258 LYS cc_start: 0.5650 (mmmt) cc_final: 0.5344 (mttm) REVERT: A 472 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6756 (tpt170) REVERT: B 199 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: B 213 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8304 (mtpp) outliers start: 23 outliers final: 21 residues processed: 129 average time/residue: 0.2567 time to fit residues: 44.8139 Evaluate side-chains 128 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP 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 584 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.174882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136056 restraints weight = 29041.554| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.42 r_work: 0.3193 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10221 Z= 0.152 Angle : 0.506 8.740 13901 Z= 0.265 Chirality : 0.035 0.242 1496 Planarity : 0.003 0.044 1662 Dihedral : 15.012 144.338 1748 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.26 % Allowed : 16.72 % Favored : 81.02 % 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: 2.91 (0.24), residues: 1132 helix: 2.80 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 82 TYR 0.016 0.001 TYR A 367 PHE 0.030 0.002 PHE A 605 TRP 0.009 0.001 TRP A 514 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00338 (10219) covalent geometry : angle 0.50592 (13897) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.56972 ( 4) hydrogen bonds : bond 0.04666 ( 735) hydrogen bonds : angle 3.96122 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5453.06 seconds wall clock time: 93 minutes 5.69 seconds (5585.69 seconds total)