Starting phenix.real_space_refine on Thu Mar 5 12:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q1u_13764/03_2026/7q1u_13764.map" } resolution = 2.7 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= 1.000 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: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 7198 2.51 5 N 1849 2.21 5 O 2010 1.98 5 H 10657 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21772 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7979 Classifications: {'peptide': 485} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 13621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 13621 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 42, 'TRANS': 829} Chain breaks: 1 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' MG': 1, 'CLR': 1, 'HD6': 1, 'HEM': 1, 'PLM': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5242 SG CYS A 324 49.621 58.920 115.967 1.00 42.74 S Time building chain proxies: 4.34, per 1000 atoms: 0.20 Number of scatterers: 21772 At special positions: 0 Unit cell: (96.1611, 91.7399, 149.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 1 26.01 S 53 16.00 P 3 15.00 Mg 1 11.99 O 2010 8.00 N 1849 7.00 C 7198 6.00 H 10657 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 816 " - pdb=" SG CYS B 889 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 15 sheets defined 54.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 57 through 70 Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 92 through 130 removed outlier: 7.368A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.030A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.658A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 removed outlier: 3.589A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.794A pdb=" N TYR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 236 through 265 Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 281 through 315 removed outlier: 3.514A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 359 through 379 removed outlier: 3.570A pdb=" N GLY A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 408 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 420 through 462 removed outlier: 3.579A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.293A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A 490 " --> pdb=" O TRP A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 122 through 143 Processing helix chain 'B' and resid 145 through 167 Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 258 through 271 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 582 through 599 removed outlier: 4.321A pdb=" N MET B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 619 Processing helix chain 'B' and resid 625 through 642 Processing helix chain 'B' and resid 670 through 682 removed outlier: 3.725A pdb=" N LYS B 676 " --> pdb=" O TRP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 699 removed outlier: 4.269A pdb=" N TRP B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 757 through 779 removed outlier: 3.594A pdb=" N VAL B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Proline residue: B 766 - end of helix Processing helix chain 'B' and resid 822 through 826 removed outlier: 3.574A pdb=" N TYR B 826 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 884 Processing helix chain 'B' and resid 895 through 899 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 30 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 removed outlier: 7.220A pdb=" N VAL B 828 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE B 844 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP B 830 " --> pdb=" O VAL B 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 107 Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.502A pdb=" N PHE B 174 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AB1, first strand: chain 'B' and resid 366 through 370 removed outlier: 6.649A pdb=" N LEU B 492 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 390 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB4, first strand: chain 'B' and resid 435 through 441 Processing sheet with id=AB5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB6, first strand: chain 'B' and resid 643 through 644 665 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 10611 1.09 - 1.34: 3493 1.34 - 1.58: 7898 1.58 - 1.83: 92 1.83 - 2.08: 6 Bond restraints: 22100 Sorted by residual: bond pdb=" CBV HD6 A 603 " pdb=" NBU HD6 A 603 " ideal model delta sigma weight residual 1.348 1.495 -0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" CBZ HD6 A 603 " pdb=" NBY HD6 A 603 " ideal model delta sigma weight residual 1.345 1.489 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C5 HD6 A 603 " pdb=" N7 HD6 A 603 " ideal model delta sigma weight residual 1.385 1.526 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C4 HD6 A 603 " pdb=" N9 HD6 A 603 " ideal model delta sigma weight residual 1.375 1.257 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C6 HD6 A 603 " pdb=" N6 HD6 A 603 " ideal model delta sigma weight residual 1.342 1.453 -0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 22095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.07: 39677 7.07 - 14.14: 12 14.14 - 21.21: 3 21.21 - 28.28: 0 28.28 - 35.35: 3 Bond angle restraints: 39695 Sorted by residual: angle pdb=" CB TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 109.00 73.65 35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 110.00 74.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 109.00 74.18 34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" OAT HD6 A 603 " pdb=" PCE HD6 A 603 " pdb=" OAU HD6 A 603 " ideal model delta sigma weight residual 120.77 101.40 19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" OAR HD6 A 603 " pdb=" PCG HD6 A 603 " pdb=" OAS HD6 A 603 " ideal model delta sigma weight residual 120.72 101.40 19.32 3.00e+00 1.11e-01 4.15e+01 ... (remaining 39690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 10273 35.88 - 71.77: 272 71.77 - 107.65: 19 107.65 - 143.53: 2 143.53 - 179.41: 3 Dihedral angle restraints: 10569 sinusoidal: 5609 harmonic: 4960 Sorted by residual: dihedral pdb=" C2B HEM A 602 " pdb=" C3B HEM A 602 " pdb=" CAB HEM A 602 " pdb=" CBB HEM A 602 " ideal model delta sinusoidal sigma weight residual -0.00 45.40 -45.40 2 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CCB HD6 A 603 " pdb=" CBZ HD6 A 603 " pdb=" CCA HD6 A 603 " pdb=" OAY HD6 A 603 " ideal model delta sinusoidal sigma weight residual 83.35 -96.06 179.41 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CCB HD6 A 603 " pdb=" CBZ HD6 A 603 " pdb=" CCA HD6 A 603 " pdb=" NBY HD6 A 603 " ideal model delta sinusoidal sigma weight residual -95.04 83.99 -179.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.994: 1635 0.994 - 1.988: 0 1.988 - 2.981: 0 2.981 - 3.975: 0 3.975 - 4.969: 1 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CCA HD6 A 603 " pdb=" CBZ HD6 A 603 " pdb=" CCB HD6 A 603 " pdb=" OAX HD6 A 603 " both_signs ideal model delta sigma weight residual False 2.47 -2.50 4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" CA TYR B 130 " pdb=" N TYR B 130 " pdb=" C TYR B 130 " pdb=" CB TYR B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CAP HD6 A 603 " pdb=" CAQ HD6 A 603 " pdb=" CCL HD6 A 603 " pdb=" OAO HD6 A 603 " both_signs ideal model delta sigma weight residual False 2.73 2.48 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1633 not shown) Planarity restraints: 3248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 352 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO A 353 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 643 " 0.007 2.00e-02 2.50e+03 9.87e-03 3.89e+00 pdb=" CG TRP B 643 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 643 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 643 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 643 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 643 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 643 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 643 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 643 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP B 643 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 643 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 643 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 643 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 643 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 643 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 609 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C GLN B 609 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN B 609 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 610 " 0.011 2.00e-02 2.50e+03 ... (remaining 3245 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 729 2.16 - 2.77: 42142 2.77 - 3.38: 65021 3.38 - 3.99: 86114 3.99 - 4.60: 133873 Nonbonded interactions: 327879 Sorted by model distance: nonbonded pdb=" OG SER B 315 " pdb="HD21 ASN B 642 " model vdw 1.551 2.450 nonbonded pdb=" HE2 HIS B 890 " pdb=" OD1 ASN B 902 " model vdw 1.567 2.450 nonbonded pdb=" HH TYR A 207 " pdb=" O LEU A 220 " model vdw 1.583 2.450 nonbonded pdb=" HA TYR B 130 " pdb=" HB3 TYR B 130 " model vdw 1.617 1.952 nonbonded pdb=" O VAL A 280 " pdb="HH12 ARG A 459 " model vdw 1.622 2.450 ... (remaining 327874 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.147 11446 Z= 0.271 Angle : 0.658 19.368 15577 Z= 0.297 Chirality : 0.129 4.969 1636 Planarity : 0.003 0.053 1953 Dihedral : 16.031 179.414 4175 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 are not related in a simple way. whole: 1.71 (0.24), residues: 1346 helix: 2.45 (0.20), residues: 659 sheet: 0.59 (0.42), residues: 157 loop : -0.40 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.028 0.001 TYR B 512 PHE 0.015 0.001 PHE A 17 TRP 0.030 0.001 TRP B 643 HIS 0.008 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00566 (11443) covalent geometry : angle 0.65761 (15573) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.49641 ( 4) hydrogen bonds : bond 0.13490 ( 660) hydrogen bonds : angle 6.42724 ( 1848) Misc. bond : bond 0.02076 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: B 840 GLU cc_start: 0.7943 (pt0) cc_final: 0.7698 (pt0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 1.3905 time to fit residues: 235.6385 Evaluate side-chains 126 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082875 restraints weight = 45071.070| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.71 r_work: 0.2878 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11446 Z= 0.167 Angle : 0.529 7.385 15577 Z= 0.276 Chirality : 0.039 0.297 1636 Planarity : 0.004 0.055 1953 Dihedral : 13.809 160.653 1678 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.87 % Allowed : 7.06 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1346 helix: 2.38 (0.19), residues: 668 sheet: 0.40 (0.40), residues: 159 loop : -0.41 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 813 TYR 0.021 0.002 TYR B 512 PHE 0.028 0.001 PHE A 17 TRP 0.013 0.001 TRP B 316 HIS 0.008 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00374 (11443) covalent geometry : angle 0.52867 (15573) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.20291 ( 4) hydrogen bonds : bond 0.04409 ( 660) hydrogen bonds : angle 4.93423 ( 1848) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 48 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7684 (ttp80) REVERT: B 487 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: B 813 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.8178 (ttt180) outliers start: 10 outliers final: 2 residues processed: 133 average time/residue: 1.3925 time to fit residues: 198.7168 Evaluate side-chains 124 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082483 restraints weight = 45069.289| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.72 r_work: 0.2870 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11446 Z= 0.177 Angle : 0.517 7.190 15577 Z= 0.269 Chirality : 0.039 0.295 1636 Planarity : 0.004 0.055 1953 Dihedral : 13.176 155.801 1678 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.05 % Allowed : 8.01 % Favored : 90.94 % 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 are not related in a simple way. whole: 1.57 (0.23), residues: 1346 helix: 2.39 (0.19), residues: 668 sheet: 0.22 (0.39), residues: 159 loop : -0.47 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.018 0.001 TYR A 180 PHE 0.026 0.001 PHE A 17 TRP 0.012 0.001 TRP B 746 HIS 0.008 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00401 (11443) covalent geometry : angle 0.51708 (15573) SS BOND : bond 0.00344 ( 2) SS BOND : angle 0.82645 ( 4) hydrogen bonds : bond 0.04142 ( 660) hydrogen bonds : angle 4.65351 ( 1848) Misc. bond : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8933 (mt) cc_final: 0.8554 (tt) REVERT: B 59 GLU cc_start: 0.7631 (tp30) cc_final: 0.7367 (tp30) REVERT: B 367 MET cc_start: 0.9161 (ttp) cc_final: 0.8893 (ttm) outliers start: 12 outliers final: 4 residues processed: 126 average time/residue: 1.4415 time to fit residues: 195.5213 Evaluate side-chains 120 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.082129 restraints weight = 44971.283| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.71 r_work: 0.2867 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11446 Z= 0.178 Angle : 0.519 7.744 15577 Z= 0.269 Chirality : 0.039 0.295 1636 Planarity : 0.004 0.051 1953 Dihedral : 12.888 155.988 1678 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.87 % Allowed : 8.28 % Favored : 90.85 % 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 are not related in a simple way. whole: 1.55 (0.23), residues: 1346 helix: 2.38 (0.19), residues: 668 sheet: 0.17 (0.38), residues: 159 loop : -0.49 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 813 TYR 0.018 0.001 TYR A 180 PHE 0.024 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00403 (11443) covalent geometry : angle 0.51914 (15573) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.81869 ( 4) hydrogen bonds : bond 0.04002 ( 660) hydrogen bonds : angle 4.52292 ( 1848) Misc. bond : bond 0.00123 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8949 (mt) cc_final: 0.8550 (tt) REVERT: B 59 GLU cc_start: 0.7624 (tp30) cc_final: 0.7406 (tp30) REVERT: B 367 MET cc_start: 0.9183 (ttp) cc_final: 0.8903 (ttm) REVERT: B 487 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7638 (tm-30) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 1.3801 time to fit residues: 182.9383 Evaluate side-chains 116 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 125 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.082692 restraints weight = 44788.756| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.72 r_work: 0.2874 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11446 Z= 0.154 Angle : 0.501 7.153 15577 Z= 0.261 Chirality : 0.039 0.299 1636 Planarity : 0.004 0.050 1953 Dihedral : 12.754 157.384 1678 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.87 % Allowed : 8.80 % Favored : 90.33 % 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 are not related in a simple way. whole: 1.58 (0.23), residues: 1346 helix: 2.43 (0.19), residues: 668 sheet: 0.07 (0.37), residues: 163 loop : -0.48 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 813 TYR 0.018 0.001 TYR A 180 PHE 0.022 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00348 (11443) covalent geometry : angle 0.50125 (15573) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.72716 ( 4) hydrogen bonds : bond 0.03843 ( 660) hydrogen bonds : angle 4.41857 ( 1848) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8965 (mt) cc_final: 0.8575 (tt) REVERT: B 59 GLU cc_start: 0.7459 (tp30) cc_final: 0.7254 (tp30) REVERT: B 84 GLU cc_start: 0.8157 (mp0) cc_final: 0.7831 (mp0) REVERT: B 367 MET cc_start: 0.9192 (ttp) cc_final: 0.8909 (ttm) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 1.3469 time to fit residues: 172.8354 Evaluate side-chains 120 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 109 GLN B 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082431 restraints weight = 44875.489| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.71 r_work: 0.2872 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11446 Z= 0.163 Angle : 0.501 7.530 15577 Z= 0.263 Chirality : 0.039 0.298 1636 Planarity : 0.003 0.049 1953 Dihedral : 12.752 156.427 1678 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.78 % Allowed : 9.06 % Favored : 90.16 % 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 are not related in a simple way. whole: 1.58 (0.23), residues: 1346 helix: 2.44 (0.19), residues: 668 sheet: 0.06 (0.37), residues: 163 loop : -0.48 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 813 TYR 0.018 0.001 TYR A 180 PHE 0.022 0.001 PHE A 17 TRP 0.012 0.001 TRP B 746 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00369 (11443) covalent geometry : angle 0.50128 (15573) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.70646 ( 4) hydrogen bonds : bond 0.03864 ( 660) hydrogen bonds : angle 4.38835 ( 1848) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8964 (mt) cc_final: 0.8573 (tt) REVERT: A 241 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 59 GLU cc_start: 0.7410 (tp30) cc_final: 0.7176 (tp30) REVERT: B 367 MET cc_start: 0.9194 (ttp) cc_final: 0.8904 (ttm) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 1.4369 time to fit residues: 178.8115 Evaluate side-chains 118 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 109 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082401 restraints weight = 44769.748| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.70 r_work: 0.2872 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11446 Z= 0.165 Angle : 0.504 7.869 15577 Z= 0.264 Chirality : 0.039 0.299 1636 Planarity : 0.003 0.048 1953 Dihedral : 12.641 153.753 1678 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.13 % Allowed : 8.71 % Favored : 90.16 % 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 are not related in a simple way. whole: 1.57 (0.23), residues: 1346 helix: 2.44 (0.19), residues: 668 sheet: 0.06 (0.37), residues: 163 loop : -0.50 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.018 0.001 TYR A 180 PHE 0.022 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00374 (11443) covalent geometry : angle 0.50421 (15573) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.67854 ( 4) hydrogen bonds : bond 0.03853 ( 660) hydrogen bonds : angle 4.36009 ( 1848) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8961 (mt) cc_final: 0.8571 (tt) REVERT: A 246 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8267 (mp) REVERT: B 84 GLU cc_start: 0.8161 (mp0) cc_final: 0.7948 (pm20) REVERT: B 367 MET cc_start: 0.9200 (ttp) cc_final: 0.8910 (ttm) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 1.3712 time to fit residues: 180.2887 Evaluate side-chains 117 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 0.0050 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.083849 restraints weight = 44673.471| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.70 r_work: 0.2883 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11446 Z= 0.140 Angle : 0.497 7.918 15577 Z= 0.260 Chirality : 0.038 0.303 1636 Planarity : 0.003 0.047 1953 Dihedral : 12.316 152.345 1678 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.87 % Allowed : 9.49 % Favored : 89.63 % 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 are not related in a simple way. whole: 1.64 (0.23), residues: 1346 helix: 2.51 (0.19), residues: 668 sheet: 0.05 (0.37), residues: 161 loop : -0.47 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.019 0.001 TYR A 180 PHE 0.019 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00316 (11443) covalent geometry : angle 0.49692 (15573) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.60445 ( 4) hydrogen bonds : bond 0.03723 ( 660) hydrogen bonds : angle 4.30528 ( 1848) Misc. bond : bond 0.00242 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8965 (mt) cc_final: 0.8578 (tt) REVERT: B 59 GLU cc_start: 0.7309 (tp30) cc_final: 0.7033 (tm-30) REVERT: B 84 GLU cc_start: 0.8156 (mp0) cc_final: 0.7951 (pm20) REVERT: B 105 GLU cc_start: 0.8888 (pt0) cc_final: 0.8663 (pt0) REVERT: B 367 MET cc_start: 0.9191 (ttp) cc_final: 0.8904 (ttm) outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 1.4339 time to fit residues: 186.9320 Evaluate side-chains 115 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083410 restraints weight = 44975.702| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.70 r_work: 0.2874 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11446 Z= 0.158 Angle : 0.505 8.162 15577 Z= 0.264 Chirality : 0.039 0.298 1636 Planarity : 0.003 0.048 1953 Dihedral : 12.170 151.521 1678 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.87 % Allowed : 9.76 % Favored : 89.37 % 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 are not related in a simple way. whole: 1.62 (0.23), residues: 1346 helix: 2.48 (0.19), residues: 668 sheet: 0.04 (0.37), residues: 161 loop : -0.48 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.018 0.001 TYR A 180 PHE 0.021 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.005 0.001 HIS B 772 Details of bonding type rmsd covalent geometry : bond 0.00360 (11443) covalent geometry : angle 0.50535 (15573) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.63660 ( 4) hydrogen bonds : bond 0.03782 ( 660) hydrogen bonds : angle 4.30659 ( 1848) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8961 (mt) cc_final: 0.8573 (tt) REVERT: B 105 GLU cc_start: 0.8899 (pt0) cc_final: 0.8659 (pt0) REVERT: B 367 MET cc_start: 0.9200 (ttp) cc_final: 0.8911 (ttm) outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 1.4455 time to fit residues: 175.9524 Evaluate side-chains 115 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.083839 restraints weight = 45041.545| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.70 r_work: 0.2883 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11446 Z= 0.145 Angle : 0.500 8.078 15577 Z= 0.261 Chirality : 0.038 0.303 1636 Planarity : 0.003 0.047 1953 Dihedral : 11.961 152.424 1678 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.70 % Allowed : 9.93 % Favored : 89.37 % 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 are not related in a simple way. whole: 1.67 (0.23), residues: 1346 helix: 2.54 (0.19), residues: 668 sheet: 0.05 (0.37), residues: 161 loop : -0.46 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.019 0.001 TYR A 180 PHE 0.018 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.005 0.001 HIS B 772 Details of bonding type rmsd covalent geometry : bond 0.00329 (11443) covalent geometry : angle 0.50021 (15573) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.58085 ( 4) hydrogen bonds : bond 0.03709 ( 660) hydrogen bonds : angle 4.27764 ( 1848) Misc. bond : bond 0.00176 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8963 (mt) cc_final: 0.8574 (tt) REVERT: B 105 GLU cc_start: 0.8897 (pt0) cc_final: 0.8670 (pt0) REVERT: B 316 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.8060 (t60) REVERT: B 367 MET cc_start: 0.9188 (ttp) cc_final: 0.8908 (ttm) outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 1.3808 time to fit residues: 172.7107 Evaluate side-chains 116 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 109 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.084257 restraints weight = 44774.958| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.70 r_work: 0.2889 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11446 Z= 0.135 Angle : 0.493 7.975 15577 Z= 0.257 Chirality : 0.038 0.304 1636 Planarity : 0.003 0.047 1953 Dihedral : 11.631 157.223 1678 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.78 % Allowed : 9.84 % Favored : 89.37 % 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 are not related in a simple way. whole: 1.70 (0.23), residues: 1346 helix: 2.57 (0.19), residues: 668 sheet: 0.05 (0.37), residues: 161 loop : -0.45 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.019 0.001 TYR A 180 PHE 0.019 0.001 PHE A 17 TRP 0.013 0.001 TRP B 746 HIS 0.005 0.001 HIS B 772 Details of bonding type rmsd covalent geometry : bond 0.00305 (11443) covalent geometry : angle 0.49278 (15573) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.56052 ( 4) hydrogen bonds : bond 0.03640 ( 660) hydrogen bonds : angle 4.24785 ( 1848) Misc. bond : bond 0.00289 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.64 seconds wall clock time: 113 minutes 43.64 seconds (6823.64 seconds total)