Starting phenix.real_space_refine on Tue Feb 11 16:15:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.map" model { file = "/net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wso_32762/02_2025/7wso_32762.cif" } resolution = 3.03 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= 0.128 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3955 2.51 5 N 1042 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6204 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2003 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 233} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 125} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1997 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 233} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135} Time building chain proxies: 4.24, per 1000 atoms: 0.68 Number of scatterers: 6204 At special positions: 0 Unit cell: (67.1, 91.3, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1174 8.00 N 1042 7.00 C 3955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 325 " distance=2.04 Simple disulfide: pdb=" SG CYS K 371 " - pdb=" SG CYS K 429 " distance=2.05 Simple disulfide: pdb=" SG CYS K 457 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS C 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 325 " distance=2.04 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 429 " distance=2.05 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 122 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 969.0 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 16 sheets defined 20.8% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'K' and resid 313 through 318 removed outlier: 3.616A pdb=" N TRP K 317 " --> pdb=" O LEU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 364 removed outlier: 3.732A pdb=" N LEU K 362 " --> pdb=" O ARG K 359 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 363 " --> pdb=" O ASP K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 418 through 423 removed outlier: 3.618A pdb=" N GLN K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 440 removed outlier: 3.875A pdb=" N TYR K 440 " --> pdb=" O HIS K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 492 removed outlier: 4.641A pdb=" N THR K 473 " --> pdb=" O TRP K 469 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE K 474 " --> pdb=" O THR K 470 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE K 475 " --> pdb=" O THR K 471 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE K 492 " --> pdb=" O THR K 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.801A pdb=" N HIS A 36 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 168 removed outlier: 3.874A pdb=" N THR A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.067A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 3.648A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 318' Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.845A pdb=" N HIS B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 440 " --> pdb=" O HIS B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.800A pdb=" N TRP B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.606A pdb=" N ILE B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 489 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.622A pdb=" N ASN C 117 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 182 removed outlier: 3.770A pdb=" N ARG C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Proline residue: C 176 - end of helix removed outlier: 3.948A pdb=" N ASP C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 243 through 247 Processing sheet with id=AA2, first strand: chain 'K' and resid 286 through 287 Processing sheet with id=AA3, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.572A pdb=" N THR K 370 " --> pdb=" O LEU K 355 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE K 408 " --> pdb=" O GLY K 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.572A pdb=" N THR K 370 " --> pdb=" O LEU K 355 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE K 408 " --> pdb=" O GLY K 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 390 through 391 Processing sheet with id=AA6, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.005A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 64 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP A 66 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.005A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA9, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB1, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.553A pdb=" N TRP B 281 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 351 through 355 removed outlier: 5.968A pdb=" N PHE B 408 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 351 through 355 removed outlier: 5.968A pdb=" N PHE B 408 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 390 through 391 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.727A pdb=" N GLY C 118 " --> pdb=" O LEU C 140 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 720 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: 1.91 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1422 1.33 - 1.46: 2020 1.46 - 1.60: 2872 1.60 - 1.73: 0 1.73 - 1.86: 46 Bond restraints: 6360 Sorted by residual: bond pdb=" CB VAL A 105 " pdb=" CG1 VAL A 105 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.47e+01 bond pdb=" CB PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 1.506 1.364 0.142 3.90e-02 6.57e+02 1.33e+01 bond pdb=" CB PRO C 50 " pdb=" CG PRO C 50 " ideal model delta sigma weight residual 1.506 1.367 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" CB GLN C 48 " pdb=" CG GLN C 48 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.76e+00 bond pdb=" CB PRO B 357 " pdb=" CG PRO B 357 " ideal model delta sigma weight residual 1.492 1.347 0.145 5.00e-02 4.00e+02 8.37e+00 ... (remaining 6355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 8515 3.95 - 7.90: 125 7.90 - 11.86: 12 11.86 - 15.81: 0 15.81 - 19.76: 2 Bond angle restraints: 8654 Sorted by residual: angle pdb=" CA LEU B 447 " pdb=" CB LEU B 447 " pdb=" CG LEU B 447 " ideal model delta sigma weight residual 116.30 136.06 -19.76 3.50e+00 8.16e-02 3.19e+01 angle pdb=" CA TYR B 411 " pdb=" CB TYR B 411 " pdb=" CG TYR B 411 " ideal model delta sigma weight residual 113.90 124.01 -10.11 1.80e+00 3.09e-01 3.16e+01 angle pdb=" CA LEU K 410 " pdb=" CB LEU K 410 " pdb=" CG LEU K 410 " ideal model delta sigma weight residual 116.30 134.75 -18.45 3.50e+00 8.16e-02 2.78e+01 angle pdb=" N LYS A 141 " pdb=" CA LYS A 141 " pdb=" C LYS A 141 " ideal model delta sigma weight residual 113.55 107.09 6.46 1.26e+00 6.30e-01 2.63e+01 angle pdb=" N ALA K 458 " pdb=" CA ALA K 458 " pdb=" C ALA K 458 " ideal model delta sigma weight residual 110.80 120.98 -10.18 2.13e+00 2.20e-01 2.28e+01 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 3594 15.02 - 30.03: 187 30.03 - 45.05: 51 45.05 - 60.07: 9 60.07 - 75.08: 6 Dihedral angle restraints: 3847 sinusoidal: 1568 harmonic: 2279 Sorted by residual: dihedral pdb=" CA CYS K 457 " pdb=" C CYS K 457 " pdb=" N ALA K 458 " pdb=" CA ALA K 458 " ideal model delta harmonic sigma weight residual 180.00 140.57 39.43 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLU B 454 " pdb=" C GLU B 454 " pdb=" N GLU B 455 " pdb=" CA GLU B 455 " ideal model delta harmonic sigma weight residual -180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA PRO A 128 " pdb=" C PRO A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 618 0.060 - 0.120: 258 0.120 - 0.180: 72 0.180 - 0.241: 16 0.241 - 0.301: 2 Chirality restraints: 966 Sorted by residual: chirality pdb=" CG LEU K 414 " pdb=" CB LEU K 414 " pdb=" CD1 LEU K 414 " pdb=" CD2 LEU K 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU C 107 " pdb=" CB LEU C 107 " pdb=" CD1 LEU C 107 " pdb=" CD2 LEU C 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE B 381 " pdb=" CA ILE B 381 " pdb=" CG1 ILE B 381 " pdb=" CG2 ILE B 381 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 963 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 104 " 0.030 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR A 104 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 104 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 104 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 104 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 104 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 104 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 104 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 78 " 0.035 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP C 78 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 78 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 78 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 78 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 78 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 78 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 78 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 78 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 86 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 87 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.042 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1996 2.86 - 3.37: 4632 3.37 - 3.88: 9122 3.88 - 4.39: 9713 4.39 - 4.90: 18455 Nonbonded interactions: 43918 Sorted by model distance: nonbonded pdb=" O SER C 71 " pdb=" NE2 GLN C 124 " model vdw 2.351 3.120 nonbonded pdb=" O MET C 163 " pdb=" OG1 THR C 166 " model vdw 2.388 3.040 nonbonded pdb=" O SER K 486 " pdb=" OG1 THR K 490 " model vdw 2.397 3.040 nonbonded pdb=" O GLN K 315 " pdb=" ND2 ASN K 319 " model vdw 2.417 3.120 nonbonded pdb=" OH TYR K 440 " pdb=" NE2 GLN K 442 " model vdw 2.427 3.120 ... (remaining 43913 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 'B' selection = (chain 'K' and (resid 241 through 491 or (resid 492 and (name N or name CA or na \ me C or name O or name CB )))) } 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: 0.850 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.014 0.145 6360 Z= 0.908 Angle : 1.295 19.760 8654 Z= 0.687 Chirality : 0.071 0.301 966 Planarity : 0.010 0.075 1111 Dihedral : 10.666 75.083 2347 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.85 % Allowed : 3.40 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.41 % 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: -2.93 (0.27), residues: 772 helix: -3.26 (0.31), residues: 124 sheet: 0.03 (0.31), residues: 277 loop : -3.14 (0.25), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP C 78 HIS 0.016 0.004 HIS C 64 PHE 0.039 0.005 PHE A 80 TYR 0.068 0.005 TYR A 104 ARG 0.023 0.002 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7513 (m-80) cc_final: 0.7099 (m-80) REVERT: K 322 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8100 (tt0) REVERT: K 324 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7557 (tttm) REVERT: K 341 SER cc_start: 0.8997 (p) cc_final: 0.8780 (t) REVERT: K 461 GLN cc_start: 0.7845 (mm110) cc_final: 0.7469 (mp10) REVERT: K 465 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8297 (pt) REVERT: B 256 MET cc_start: 0.7588 (mtm) cc_final: 0.6680 (mmt) REVERT: B 348 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8220 (mtt180) REVERT: B 390 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6814 (mt0) REVERT: C 67 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.5544 (pmt) REVERT: C 83 ASP cc_start: 0.5885 (m-30) cc_final: 0.5628 (m-30) REVERT: C 87 GLN cc_start: 0.7651 (mt0) cc_final: 0.6975 (mm110) outliers start: 6 outliers final: 1 residues processed: 134 average time/residue: 0.2139 time to fit residues: 36.4263 Evaluate side-chains 95 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 67 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS K 329 ASN K 394 ASN K 439 HIS A 36 HIS A 127 GLN B 272 HIS B 329 ASN B 394 ASN B 425 ASN B 439 HIS B 442 GLN C 48 GLN C 68 ASN C 165 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.191806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111612 restraints weight = 7028.891| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.91 r_work: 0.2966 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6360 Z= 0.196 Angle : 0.610 8.209 8654 Z= 0.318 Chirality : 0.045 0.154 966 Planarity : 0.006 0.060 1111 Dihedral : 5.704 46.846 837 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.12 % Allowed : 6.94 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.76 (0.29), residues: 772 helix: -1.34 (0.43), residues: 130 sheet: 0.56 (0.32), residues: 282 loop : -2.65 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.005 0.001 HIS K 314 PHE 0.013 0.001 PHE B 409 TYR 0.017 0.001 TYR A 104 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7552 (m-80) cc_final: 0.7094 (m-80) REVERT: K 316 ASP cc_start: 0.7944 (m-30) cc_final: 0.7471 (t0) REVERT: K 319 ASN cc_start: 0.8496 (m-40) cc_final: 0.8004 (m110) REVERT: K 322 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8115 (tt0) REVERT: K 324 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7441 (tttm) REVERT: K 341 SER cc_start: 0.8886 (p) cc_final: 0.8622 (t) REVERT: A 116 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8201 (mt0) REVERT: A 136 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.5592 (mpp) REVERT: B 256 MET cc_start: 0.7469 (mtm) cc_final: 0.6498 (mmt) REVERT: B 292 LYS cc_start: 0.6909 (ttmt) cc_final: 0.6214 (mttm) REVERT: B 324 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7047 (ttpp) REVERT: B 348 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8429 (mtt180) REVERT: B 404 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8297 (p) REVERT: C 87 GLN cc_start: 0.8037 (mt0) cc_final: 0.7577 (mm110) REVERT: C 93 LYS cc_start: 0.8698 (mptt) cc_final: 0.8445 (mmtt) outliers start: 15 outliers final: 7 residues processed: 114 average time/residue: 0.2066 time to fit residues: 30.1698 Evaluate side-chains 100 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS A 117 GLN B 365 ASN C 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.192402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112511 restraints weight = 7100.073| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.90 r_work: 0.3038 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6360 Z= 0.154 Angle : 0.546 7.117 8654 Z= 0.279 Chirality : 0.043 0.152 966 Planarity : 0.005 0.050 1111 Dihedral : 5.070 45.842 835 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.56 % Allowed : 9.77 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.26 (0.30), residues: 772 helix: -0.60 (0.45), residues: 130 sheet: 0.84 (0.31), residues: 289 loop : -2.49 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 469 HIS 0.002 0.001 HIS A 71 PHE 0.009 0.001 PHE K 376 TYR 0.014 0.001 TYR B 411 ARG 0.003 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7534 (m-80) cc_final: 0.7110 (m-80) REVERT: K 319 ASN cc_start: 0.8459 (m-40) cc_final: 0.7861 (m110) REVERT: K 322 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8142 (tt0) REVERT: K 323 TYR cc_start: 0.8260 (m-80) cc_final: 0.8031 (m-80) REVERT: K 324 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7557 (tttm) REVERT: K 341 SER cc_start: 0.8778 (p) cc_final: 0.8552 (t) REVERT: K 348 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7927 (mtm180) REVERT: A 95 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8474 (m-40) REVERT: A 97 ASN cc_start: 0.7560 (p0) cc_final: 0.7307 (p0) REVERT: A 136 MET cc_start: 0.6418 (pmt) cc_final: 0.5822 (mpp) REVERT: B 256 MET cc_start: 0.7447 (mtm) cc_final: 0.6456 (mmt) REVERT: B 292 LYS cc_start: 0.6752 (ttmt) cc_final: 0.6084 (mttm) REVERT: B 324 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7062 (ttpp) REVERT: B 348 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8416 (mtt180) REVERT: B 404 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 87 GLN cc_start: 0.7949 (mt0) cc_final: 0.7489 (mm110) REVERT: C 93 LYS cc_start: 0.8732 (mptt) cc_final: 0.8458 (mmtt) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.1957 time to fit residues: 26.5830 Evaluate side-chains 96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN C 68 ASN C 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.189452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110891 restraints weight = 7020.003| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.77 r_work: 0.2987 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6360 Z= 0.198 Angle : 0.577 6.918 8654 Z= 0.296 Chirality : 0.044 0.157 966 Planarity : 0.005 0.049 1111 Dihedral : 5.110 43.920 835 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.69 % Allowed : 9.77 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.89 (0.30), residues: 772 helix: -0.18 (0.47), residues: 130 sheet: 1.07 (0.31), residues: 289 loop : -2.31 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 78 HIS 0.004 0.001 HIS B 439 PHE 0.014 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7596 (m-80) cc_final: 0.7273 (m-80) REVERT: K 322 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8270 (tt0) REVERT: K 324 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7680 (tttm) REVERT: K 338 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6584 (mttm) REVERT: K 346 GLN cc_start: 0.8639 (tp40) cc_final: 0.8302 (tt0) REVERT: A 95 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8572 (m-40) REVERT: A 136 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5772 (mpp) REVERT: B 256 MET cc_start: 0.7609 (mtm) cc_final: 0.6573 (mmt) REVERT: B 292 LYS cc_start: 0.6980 (ttmt) cc_final: 0.6276 (mttm) REVERT: B 324 LYS cc_start: 0.7582 (ttmt) cc_final: 0.6791 (tptt) REVERT: B 348 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8425 (mtt180) REVERT: B 404 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 454 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: C 68 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7938 (p0) REVERT: C 87 GLN cc_start: 0.8115 (mt0) cc_final: 0.7606 (mm110) REVERT: C 93 LYS cc_start: 0.8747 (mptt) cc_final: 0.8470 (mmtt) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.1980 time to fit residues: 24.9205 Evaluate side-chains 99 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN ** C 165 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.186074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108075 restraints weight = 7006.628| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.93 r_work: 0.2928 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6360 Z= 0.401 Angle : 0.717 10.099 8654 Z= 0.372 Chirality : 0.049 0.198 966 Planarity : 0.006 0.051 1111 Dihedral : 5.598 39.176 835 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.83 % Allowed : 11.47 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.93 (0.30), residues: 772 helix: -0.15 (0.47), residues: 132 sheet: 1.05 (0.31), residues: 288 loop : -2.37 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 78 HIS 0.008 0.002 HIS B 439 PHE 0.024 0.002 PHE K 376 TYR 0.024 0.002 TYR B 411 ARG 0.002 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7462 (m-80) cc_final: 0.7240 (m-80) REVERT: K 322 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8175 (tt0) REVERT: K 324 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7631 (tttm) REVERT: K 338 LYS cc_start: 0.6833 (mmtt) cc_final: 0.6625 (mttm) REVERT: K 346 GLN cc_start: 0.8600 (tp40) cc_final: 0.8297 (tt0) REVERT: K 462 ASP cc_start: 0.8246 (p0) cc_final: 0.7638 (t0) REVERT: K 465 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8350 (pp) REVERT: A 43 MET cc_start: 0.8948 (mtp) cc_final: 0.8693 (mtm) REVERT: A 136 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5660 (mpp) REVERT: A 138 GLU cc_start: 0.8096 (tp30) cc_final: 0.7896 (tp30) REVERT: B 256 MET cc_start: 0.7502 (mtm) cc_final: 0.6493 (mmt) REVERT: B 292 LYS cc_start: 0.6966 (ttmt) cc_final: 0.6331 (mttm) REVERT: B 324 LYS cc_start: 0.7606 (ttmt) cc_final: 0.6794 (tptt) REVERT: B 348 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8454 (mtt180) REVERT: B 404 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 85 ASN cc_start: 0.7831 (m-40) cc_final: 0.7408 (p0) REVERT: C 87 GLN cc_start: 0.8034 (mt0) cc_final: 0.7489 (mm110) REVERT: C 93 LYS cc_start: 0.8745 (mptt) cc_final: 0.8453 (mmtt) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 0.1994 time to fit residues: 26.1539 Evaluate side-chains 101 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 164 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN ** C 165 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.187946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107678 restraints weight = 6977.301| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.85 r_work: 0.2956 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6360 Z= 0.254 Angle : 0.613 7.778 8654 Z= 0.317 Chirality : 0.045 0.164 966 Planarity : 0.005 0.050 1111 Dihedral : 5.268 43.630 835 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 11.61 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.78 (0.30), residues: 772 helix: -0.01 (0.47), residues: 132 sheet: 1.14 (0.31), residues: 287 loop : -2.27 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 34 HIS 0.005 0.001 HIS B 439 PHE 0.016 0.002 PHE K 376 TYR 0.019 0.001 TYR B 411 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.686 Fit side-chains REVERT: K 322 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8234 (tt0) REVERT: K 324 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7649 (tttm) REVERT: K 338 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6612 (mttm) REVERT: K 346 GLN cc_start: 0.8669 (tp40) cc_final: 0.8388 (tt0) REVERT: K 462 ASP cc_start: 0.8384 (p0) cc_final: 0.7654 (t0) REVERT: A 43 MET cc_start: 0.9002 (mtp) cc_final: 0.8752 (mtm) REVERT: A 112 ASN cc_start: 0.8214 (m-40) cc_final: 0.7281 (p0) REVERT: A 136 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5792 (mpp) REVERT: B 256 MET cc_start: 0.7565 (mtm) cc_final: 0.6533 (mmt) REVERT: B 292 LYS cc_start: 0.7086 (ttmt) cc_final: 0.6538 (mttm) REVERT: B 348 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8473 (mtt180) REVERT: B 404 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8341 (p) REVERT: C 85 ASN cc_start: 0.8024 (m-40) cc_final: 0.7540 (p0) REVERT: C 87 GLN cc_start: 0.8162 (mt0) cc_final: 0.7599 (mm110) REVERT: C 93 LYS cc_start: 0.8768 (mptt) cc_final: 0.8488 (mmtt) outliers start: 21 outliers final: 17 residues processed: 97 average time/residue: 0.1942 time to fit residues: 24.9439 Evaluate side-chains 102 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN ** C 165 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.185952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111673 restraints weight = 6958.351| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.33 r_work: 0.2916 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6360 Z= 0.297 Angle : 0.645 8.804 8654 Z= 0.335 Chirality : 0.046 0.169 966 Planarity : 0.005 0.051 1111 Dihedral : 5.384 46.962 835 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.97 % Allowed : 12.32 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.72 (0.30), residues: 772 helix: 0.04 (0.47), residues: 132 sheet: 1.17 (0.31), residues: 288 loop : -2.23 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 34 HIS 0.006 0.001 HIS B 439 PHE 0.018 0.002 PHE K 376 TYR 0.021 0.002 TYR B 411 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.797 Fit side-chains REVERT: K 322 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8168 (tt0) REVERT: K 324 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7503 (tttm) REVERT: K 346 GLN cc_start: 0.8607 (tp40) cc_final: 0.8328 (tt0) REVERT: K 462 ASP cc_start: 0.8303 (p0) cc_final: 0.7427 (t0) REVERT: A 112 ASN cc_start: 0.8222 (m-40) cc_final: 0.7349 (p0) REVERT: A 136 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5741 (mpp) REVERT: B 250 LYS cc_start: 0.8093 (mttp) cc_final: 0.7750 (mtpt) REVERT: B 256 MET cc_start: 0.7431 (mtm) cc_final: 0.6390 (mmt) REVERT: B 292 LYS cc_start: 0.6967 (ttmt) cc_final: 0.6467 (mttm) REVERT: B 319 ASN cc_start: 0.7610 (m-40) cc_final: 0.7288 (m110) REVERT: B 348 ARG cc_start: 0.8716 (mtt90) cc_final: 0.8408 (mtt180) REVERT: B 404 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 85 ASN cc_start: 0.7850 (m-40) cc_final: 0.7412 (p0) REVERT: C 87 GLN cc_start: 0.8035 (mt0) cc_final: 0.7469 (mm110) REVERT: C 93 LYS cc_start: 0.8738 (mptt) cc_final: 0.8447 (mmtt) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 0.1960 time to fit residues: 26.2606 Evaluate side-chains 104 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 50 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN B 442 GLN C 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.189206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111144 restraints weight = 6968.778| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.78 r_work: 0.3049 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6360 Z= 0.145 Angle : 0.527 6.801 8654 Z= 0.271 Chirality : 0.043 0.152 966 Planarity : 0.005 0.051 1111 Dihedral : 4.757 43.792 835 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.27 % Allowed : 12.89 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.60 (0.30), residues: 772 helix: -0.08 (0.46), residues: 138 sheet: 1.27 (0.31), residues: 290 loop : -2.12 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.002 0.001 HIS B 439 PHE 0.011 0.001 PHE B 409 TYR 0.012 0.001 TYR B 411 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.680 Fit side-chains REVERT: K 322 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8191 (tt0) REVERT: K 324 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7417 (tttm) REVERT: K 346 GLN cc_start: 0.8620 (tp40) cc_final: 0.8341 (tt0) REVERT: A 37 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8295 (mmtm) REVERT: A 43 MET cc_start: 0.9000 (mtp) cc_final: 0.8738 (mtm) REVERT: A 112 ASN cc_start: 0.8176 (m-40) cc_final: 0.7299 (p0) REVERT: A 136 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.6040 (mmp) REVERT: B 256 MET cc_start: 0.7475 (mtm) cc_final: 0.6448 (mmt) REVERT: B 292 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6519 (mttm) REVERT: B 348 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8504 (mtt180) REVERT: B 454 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.5843 (pm20) REVERT: C 85 ASN cc_start: 0.8099 (m-40) cc_final: 0.7470 (p0) REVERT: C 87 GLN cc_start: 0.8082 (mt0) cc_final: 0.7552 (mm110) REVERT: C 93 LYS cc_start: 0.8767 (mptt) cc_final: 0.8495 (mmtt) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 0.1842 time to fit residues: 23.8098 Evaluate side-chains 103 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN ** C 165 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.189494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109335 restraints weight = 7011.145| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.85 r_work: 0.3005 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6360 Z= 0.201 Angle : 0.567 7.165 8654 Z= 0.293 Chirality : 0.044 0.158 966 Planarity : 0.005 0.046 1111 Dihedral : 4.949 45.420 835 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.55 % Allowed : 12.89 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.48 (0.30), residues: 772 helix: -0.01 (0.46), residues: 138 sheet: 1.36 (0.31), residues: 289 loop : -2.05 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 281 HIS 0.004 0.001 HIS B 439 PHE 0.013 0.001 PHE K 376 TYR 0.016 0.001 TYR B 411 ARG 0.001 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.699 Fit side-chains REVERT: K 322 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8060 (tt0) REVERT: K 324 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7484 (tttm) REVERT: A 57 ASN cc_start: 0.7055 (t0) cc_final: 0.6848 (t0) REVERT: A 112 ASN cc_start: 0.8196 (m-40) cc_final: 0.7355 (p0) REVERT: B 256 MET cc_start: 0.7389 (mtm) cc_final: 0.6369 (mmt) REVERT: B 292 LYS cc_start: 0.7031 (ttmt) cc_final: 0.6404 (mmtm) REVERT: B 348 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8447 (mtt180) REVERT: C 85 ASN cc_start: 0.7914 (m-40) cc_final: 0.7390 (p0) REVERT: C 87 GLN cc_start: 0.7955 (mt0) cc_final: 0.7448 (mm110) REVERT: C 93 LYS cc_start: 0.8756 (mptt) cc_final: 0.8475 (mmtt) outliers start: 18 outliers final: 17 residues processed: 95 average time/residue: 0.1808 time to fit residues: 23.0129 Evaluate side-chains 98 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.190254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109451 restraints weight = 7075.228| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.87 r_work: 0.2975 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6360 Z= 0.203 Angle : 0.572 7.124 8654 Z= 0.294 Chirality : 0.044 0.159 966 Planarity : 0.005 0.047 1111 Dihedral : 4.922 45.178 835 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.41 % Allowed : 12.89 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.44 (0.30), residues: 772 helix: 0.07 (0.46), residues: 138 sheet: 1.36 (0.31), residues: 289 loop : -2.01 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 281 HIS 0.004 0.001 HIS B 439 PHE 0.013 0.001 PHE K 376 TYR 0.016 0.001 TYR B 411 ARG 0.001 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.707 Fit side-chains REVERT: K 322 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8136 (tt0) REVERT: K 324 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7511 (tttm) REVERT: K 462 ASP cc_start: 0.8308 (p0) cc_final: 0.7303 (t0) REVERT: A 57 ASN cc_start: 0.7117 (t0) cc_final: 0.6910 (t0) REVERT: A 112 ASN cc_start: 0.8152 (m-40) cc_final: 0.7280 (p0) REVERT: A 136 MET cc_start: 0.6480 (mmp) cc_final: 0.5770 (mpp) REVERT: B 256 MET cc_start: 0.7434 (mtm) cc_final: 0.6392 (mmt) REVERT: B 292 LYS cc_start: 0.6972 (ttmt) cc_final: 0.6344 (mmtm) REVERT: B 348 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8505 (mtt180) REVERT: B 404 SER cc_start: 0.8626 (m) cc_final: 0.8359 (p) REVERT: C 85 ASN cc_start: 0.8106 (m-40) cc_final: 0.7461 (p0) REVERT: C 87 GLN cc_start: 0.8085 (mt0) cc_final: 0.7538 (mm110) REVERT: C 93 LYS cc_start: 0.8769 (mptt) cc_final: 0.8505 (mmtt) outliers start: 17 outliers final: 17 residues processed: 94 average time/residue: 0.1896 time to fit residues: 23.6948 Evaluate side-chains 99 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.188890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108357 restraints weight = 7097.583| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.88 r_work: 0.2965 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6360 Z= 0.216 Angle : 0.583 7.391 8654 Z= 0.301 Chirality : 0.044 0.162 966 Planarity : 0.005 0.044 1111 Dihedral : 4.991 45.221 835 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.69 % Allowed : 12.61 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.42 (0.30), residues: 772 helix: 0.09 (0.46), residues: 138 sheet: 1.26 (0.31), residues: 295 loop : -1.94 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 281 HIS 0.004 0.001 HIS B 439 PHE 0.014 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.002 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.72 seconds wall clock time: 78 minutes 22.38 seconds (4702.38 seconds total)