Starting phenix.real_space_refine on Tue May 20 08:23:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvo_47213/05_2025/9dvo_47213_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvo_47213/05_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_47213/05_2025/9dvo_47213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvo_47213/05_2025/9dvo_47213.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvo_47213/05_2025/9dvo_47213_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvo_47213/05_2025/9dvo_47213_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.53, per 1000 atoms: 0.54 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: 5.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 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: 7.13 Time building geometry restraints manager: 6.75 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 625 or resid 701 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: 3.090 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: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.400 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (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 TRP 0.008 0.001 TRP B 528 HIS 0.004 0.001 HIS B 504 PHE 0.015 0.001 PHE A 487 TYR 0.024 0.001 TYR A 483 ARG 0.003 0.000 ARG B 157 Details of bonding type rmsd hydrogen bonds : bond 0.11440 ( 735) hydrogen bonds : angle 4.61762 ( 2172) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.53129 ( 4) covalent geometry : bond 0.00610 (10219) covalent geometry : angle 1.06417 (13897) *********************** 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 : 1.389 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: 0.6923 (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: 0.5813 time to fit residues: 133.6215 Evaluate side-chains 132 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 103 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 127 ASN B 441 HIS B 616 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.177580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137473 restraints weight = 29420.699| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.55 r_work: 0.3318 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10221 Z= 0.142 Angle : 0.503 6.171 13901 Z= 0.262 Chirality : 0.034 0.152 1496 Planarity : 0.004 0.026 1662 Dihedral : 18.852 176.249 1756 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.25), residues: 1132 helix: 3.10 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 528 HIS 0.009 0.001 HIS B 504 PHE 0.022 0.001 PHE A 605 TYR 0.014 0.001 TYR A 483 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 735) hydrogen bonds : angle 4.20452 ( 2172) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.57237 ( 4) covalent geometry : bond 0.00295 (10219) covalent geometry : angle 0.50261 (13897) *********************** 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 150 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7606 (mttp) REVERT: A 417 TYR cc_start: 0.7378 (t80) cc_final: 0.7125 (t80) REVERT: A 472 ARG cc_start: 0.7337 (mtp180) cc_final: 0.6717 (tpt170) REVERT: A 508 MET cc_start: 0.6329 (mmt) cc_final: 0.5922 (tpp) REVERT: B 199 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: B 508 MET cc_start: 0.6495 (mmt) cc_final: 0.5561 (mmm) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.5722 time to fit residues: 111.3902 Evaluate side-chains 135 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 620 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN B 441 HIS B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128729 restraints weight = 29248.365| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.53 r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10221 Z= 0.186 Angle : 0.535 6.988 13901 Z= 0.282 Chirality : 0.037 0.261 1496 Planarity : 0.004 0.038 1662 Dihedral : 17.670 164.367 1750 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 16.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.25), residues: 1132 helix: 2.88 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.57 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 528 HIS 0.007 0.001 HIS B 504 PHE 0.040 0.002 PHE A 605 TYR 0.015 0.002 TYR A 352 ARG 0.005 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 735) hydrogen bonds : angle 4.14132 ( 2172) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.54381 ( 4) covalent geometry : bond 0.00418 (10219) covalent geometry : angle 0.53497 (13897) *********************** 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 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7661 (mmm) cc_final: 0.7417 (tpt) REVERT: A 2 LYS cc_start: 0.8466 (mtpt) cc_final: 0.7833 (mttp) REVERT: A 59 PHE cc_start: 0.6613 (m-10) cc_final: 0.6118 (m-80) REVERT: A 472 ARG cc_start: 0.7367 (mtp180) cc_final: 0.6705 (tpt170) REVERT: A 508 MET cc_start: 0.6263 (mmt) cc_final: 0.5700 (tpp) REVERT: B 199 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: B 508 MET cc_start: 0.6555 (mmt) cc_final: 0.6139 (mmm) outliers start: 24 outliers final: 15 residues processed: 142 average time/residue: 0.6298 time to fit residues: 116.8977 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 : 1.394 ------------------------------------------------------------------------------- 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 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 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 410 LEU Chi-restraints excluded: chain B residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 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 = 0.3843 r_free = 0.3843 target = 0.171666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130224 restraints weight = 29412.456| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.56 r_work: 0.3221 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2203 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= 0.140 Angle : 0.487 7.827 13901 Z= 0.256 Chirality : 0.035 0.234 1496 Planarity : 0.003 0.030 1662 Dihedral : 17.215 158.525 1748 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.97 % Allowed : 16.72 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.25), residues: 1132 helix: 2.93 (0.16), residues: 879 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.003 0.001 HIS B 504 PHE 0.027 0.001 PHE A 605 TYR 0.011 0.001 TYR A 483 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 735) hydrogen bonds : angle 4.01009 ( 2172) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.50641 ( 4) covalent geometry : bond 0.00308 (10219) covalent geometry : angle 0.48693 (13897) *********************** 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 137 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7714 (mmm) cc_final: 0.7428 (tpt) REVERT: A 2 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7922 (mttp) REVERT: A 59 PHE cc_start: 0.6708 (m-10) cc_final: 0.6205 (m-80) REVERT: A 83 ARG cc_start: 0.8083 (tpt-90) cc_final: 0.7787 (tpt170) REVERT: A 472 ARG cc_start: 0.7320 (mtp180) cc_final: 0.6675 (tpt170) REVERT: A 508 MET cc_start: 0.6224 (mmt) cc_final: 0.5718 (tpp) REVERT: B 199 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6699 (mt-10) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.5890 time to fit residues: 105.5231 Evaluate side-chains 132 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 509 VAL Chi-restraints excluded: chain A residue 548 ARG 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 298 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.168542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.126474 restraints weight = 29370.873| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.49 r_work: 0.3156 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10221 Z= 0.195 Angle : 0.538 7.925 13901 Z= 0.284 Chirality : 0.037 0.272 1496 Planarity : 0.004 0.043 1662 Dihedral : 16.785 146.397 1748 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.75 % Allowed : 15.93 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.24), residues: 1132 helix: 2.68 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.004 0.001 HIS B 313 PHE 0.036 0.002 PHE A 605 TYR 0.014 0.002 TYR A 483 ARG 0.004 0.001 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 735) hydrogen bonds : angle 4.11952 ( 2172) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.43119 ( 4) covalent geometry : bond 0.00441 (10219) covalent geometry : angle 0.53833 (13897) *********************** 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 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7619 (mmm) cc_final: 0.7295 (tpt) REVERT: A 2 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8032 (mttp) REVERT: A 59 PHE cc_start: 0.7048 (m-10) cc_final: 0.6646 (m-80) REVERT: A 83 ARG cc_start: 0.8099 (tpt-90) cc_final: 0.7783 (tpt170) REVERT: A 472 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6709 (tpt170) REVERT: A 508 MET cc_start: 0.6324 (mmt) cc_final: 0.5868 (tpp) REVERT: B 199 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 273 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7996 (ptp90) outliers start: 28 outliers final: 22 residues processed: 143 average time/residue: 0.5946 time to fit residues: 113.6612 Evaluate side-chains 137 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 8 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.176658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138117 restraints weight = 29007.161| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.37 r_work: 0.3243 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10221 Z= 0.129 Angle : 0.492 8.707 13901 Z= 0.258 Chirality : 0.034 0.213 1496 Planarity : 0.003 0.037 1662 Dihedral : 16.218 142.034 1748 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.24), residues: 1132 helix: 2.86 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS B 299 PHE 0.027 0.001 PHE A 605 TYR 0.011 0.001 TYR B 148 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 735) hydrogen bonds : angle 3.97299 ( 2172) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.63186 ( 4) covalent geometry : bond 0.00277 (10219) covalent geometry : angle 0.49209 (13897) *********************** 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 135 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7702 (mmm) cc_final: 0.7336 (tpt) REVERT: A 59 PHE cc_start: 0.6979 (m-10) cc_final: 0.6564 (m-80) REVERT: A 83 ARG cc_start: 0.8046 (tpt-90) cc_final: 0.7746 (tpt170) REVERT: A 472 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6730 (tpt170) REVERT: A 508 MET cc_start: 0.6249 (mmt) cc_final: 0.5814 (tpp) REVERT: B 128 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 199 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: B 309 SER cc_start: 0.9087 (t) cc_final: 0.8817 (p) outliers start: 23 outliers final: 16 residues processed: 132 average time/residue: 0.5696 time to fit residues: 101.2199 Evaluate side-chains 129 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 445 TYR Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 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 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.167905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125485 restraints weight = 29316.775| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.58 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2768 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= 0.180 Angle : 0.525 8.424 13901 Z= 0.277 Chirality : 0.036 0.251 1496 Planarity : 0.004 0.042 1662 Dihedral : 15.973 140.539 1748 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.24), residues: 1132 helix: 2.72 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.004 0.001 HIS B 313 PHE 0.035 0.002 PHE A 605 TYR 0.013 0.001 TYR A 483 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 735) hydrogen bonds : angle 4.04684 ( 2172) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.49257 ( 4) covalent geometry : bond 0.00408 (10219) covalent geometry : angle 0.52452 (13897) *********************** 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 134 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7547 (mmm) cc_final: 0.7305 (tpt) REVERT: A 83 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7672 (tpt170) REVERT: A 258 LYS cc_start: 0.5525 (mmmt) cc_final: 0.5263 (mttm) REVERT: A 472 ARG cc_start: 0.7345 (mtp180) cc_final: 0.6611 (tpt170) REVERT: A 508 MET cc_start: 0.6189 (mmt) cc_final: 0.5774 (tpp) REVERT: B 128 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7628 (tt) REVERT: B 199 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: B 309 SER cc_start: 0.9090 (t) cc_final: 0.8737 (p) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.5911 time to fit residues: 105.4005 Evaluate side-chains 130 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 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 445 TYR Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.168075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.125403 restraints weight = 29353.061| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.56 r_work: 0.3148 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2836 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= 0.155 Angle : 0.505 8.654 13901 Z= 0.266 Chirality : 0.035 0.236 1496 Planarity : 0.004 0.042 1662 Dihedral : 15.370 141.373 1748 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.06 % Allowed : 16.52 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.24), residues: 1132 helix: 2.79 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.003 0.001 HIS A 6 PHE 0.030 0.002 PHE A 605 TYR 0.012 0.001 TYR A 367 ARG 0.004 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 735) hydrogen bonds : angle 3.99488 ( 2172) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.61121 ( 4) covalent geometry : bond 0.00346 (10219) covalent geometry : angle 0.50485 (13897) *********************** 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 132 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7516 (mmm) cc_final: 0.7263 (tpt) REVERT: A 83 ARG cc_start: 0.7979 (tpt-90) cc_final: 0.7669 (tpt170) REVERT: A 258 LYS cc_start: 0.5581 (mmmt) cc_final: 0.5307 (mttm) REVERT: A 472 ARG cc_start: 0.7333 (mtp180) cc_final: 0.6629 (tpt170) REVERT: A 508 MET cc_start: 0.6185 (mmt) cc_final: 0.5785 (tpp) REVERT: B 199 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: B 309 SER cc_start: 0.9092 (t) cc_final: 0.8743 (p) outliers start: 21 outliers final: 16 residues processed: 129 average time/residue: 0.5624 time to fit residues: 97.8045 Evaluate side-chains 125 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 445 TYR Chi-restraints excluded: chain B residue 599 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.168384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.126300 restraints weight = 29155.512| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.52 r_work: 0.3167 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10221 Z= 0.146 Angle : 0.501 8.723 13901 Z= 0.263 Chirality : 0.035 0.238 1496 Planarity : 0.003 0.042 1662 Dihedral : 15.163 141.505 1748 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.97 % Allowed : 16.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.24), residues: 1132 helix: 2.79 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.003 0.001 HIS B 313 PHE 0.029 0.002 PHE A 605 TYR 0.015 0.001 TYR A 367 ARG 0.005 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 735) hydrogen bonds : angle 3.97300 ( 2172) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.55658 ( 4) covalent geometry : bond 0.00321 (10219) covalent geometry : angle 0.50100 (13897) *********************** 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 129 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7571 (mmm) cc_final: 0.7309 (tpt) REVERT: A 83 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7712 (tpt170) REVERT: A 258 LYS cc_start: 0.5604 (mmmt) cc_final: 0.5325 (mttm) REVERT: A 472 ARG cc_start: 0.7357 (mtp180) cc_final: 0.6648 (tpt170) REVERT: A 508 MET cc_start: 0.6171 (mmt) cc_final: 0.5775 (tpp) REVERT: B 199 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: B 273 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7958 (ptp90) REVERT: B 309 SER cc_start: 0.9083 (t) cc_final: 0.8762 (p) outliers start: 20 outliers final: 17 residues processed: 127 average time/residue: 0.5852 time to fit residues: 99.7621 Evaluate side-chains 128 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.166245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.125314 restraints weight = 29372.232| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.50 r_work: 0.3140 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10221 Z= 0.178 Angle : 0.526 8.616 13901 Z= 0.277 Chirality : 0.036 0.261 1496 Planarity : 0.004 0.045 1662 Dihedral : 15.195 145.534 1748 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.97 % Allowed : 16.52 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.24), residues: 1132 helix: 2.69 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.004 0.001 HIS B 313 PHE 0.033 0.002 PHE A 605 TYR 0.016 0.001 TYR A 367 ARG 0.007 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 735) hydrogen bonds : angle 4.03732 ( 2172) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.48768 ( 4) covalent geometry : bond 0.00404 (10219) covalent geometry : angle 0.52612 (13897) ********************** 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 129 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8026 (tpt-90) cc_final: 0.7728 (tpt170) REVERT: A 258 LYS cc_start: 0.5592 (mmmt) cc_final: 0.5323 (mttm) REVERT: A 472 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6620 (tpt170) REVERT: A 508 MET cc_start: 0.6182 (mmt) cc_final: 0.5827 (tpp) REVERT: B 199 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: B 273 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7952 (ptp90) REVERT: B 309 SER cc_start: 0.9088 (t) cc_final: 0.8751 (p) outliers start: 20 outliers final: 17 residues processed: 127 average time/residue: 0.5733 time to fit residues: 97.1416 Evaluate side-chains 126 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 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 82 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.168921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127841 restraints weight = 29247.997| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.47 r_work: 0.3174 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2940 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= 0.131 Angle : 0.492 8.903 13901 Z= 0.258 Chirality : 0.034 0.228 1496 Planarity : 0.003 0.043 1662 Dihedral : 14.901 142.496 1748 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.87 % Allowed : 16.62 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.24), residues: 1132 helix: 2.84 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS A 6 PHE 0.027 0.001 PHE A 605 TYR 0.016 0.001 TYR A 367 ARG 0.005 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 735) hydrogen bonds : angle 3.93316 ( 2172) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.63353 ( 4) covalent geometry : bond 0.00283 (10219) covalent geometry : angle 0.49175 (13897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10789.80 seconds wall clock time: 185 minutes 8.82 seconds (11108.82 seconds total)