Starting phenix.real_space_refine on Mon Sep 23 23:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_32762.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_32762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_32762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_32762.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/09_2024/7wso_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-5461/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: 4.15, per 1000 atoms: 0.67 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: 1.31 Conformation dependent library (CDL) restraints added in 891.6 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: 0.80 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: 1.93 Time building geometry restraints manager: 1.56 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: 0.830 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.900 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.702 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: 0.2047 time to fit residues: 34.9674 Evaluate side-chains 95 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7500 (m-80) cc_final: 0.7074 (m-80) REVERT: K 316 ASP cc_start: 0.7789 (m-30) cc_final: 0.7375 (t0) REVERT: K 319 ASN cc_start: 0.8579 (m-40) cc_final: 0.8121 (m110) REVERT: K 322 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8078 (tt0) REVERT: K 324 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7613 (tttm) REVERT: K 341 SER cc_start: 0.8969 (p) cc_final: 0.8738 (t) REVERT: A 136 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.5571 (mpp) REVERT: B 256 MET cc_start: 0.7377 (mtm) cc_final: 0.6589 (mmt) REVERT: B 292 LYS cc_start: 0.7393 (ttmt) cc_final: 0.6593 (mttm) REVERT: B 324 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7352 (ttpp) REVERT: B 348 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8292 (mtt180) REVERT: B 404 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8211 (p) REVERT: C 87 GLN cc_start: 0.7394 (mt0) cc_final: 0.6885 (mm110) REVERT: C 93 LYS cc_start: 0.8619 (mptt) cc_final: 0.8347 (mmtt) outliers start: 15 outliers final: 7 residues processed: 114 average time/residue: 0.2022 time to fit residues: 29.8293 Evaluate side-chains 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. 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 38 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 57 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 68 ASN C 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6360 Z= 0.206 Angle : 0.595 7.511 8654 Z= 0.306 Chirality : 0.045 0.159 966 Planarity : 0.005 0.052 1111 Dihedral : 5.372 44.041 835 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.27 % Allowed : 9.49 % Favored : 88.24 % 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: -1.31 (0.29), residues: 772 helix: -0.60 (0.46), residues: 130 sheet: 0.82 (0.32), residues: 282 loop : -2.48 (0.28), residues: 360 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 0.015 0.001 PHE K 376 TYR 0.018 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 108 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7510 (m-80) cc_final: 0.7115 (m-80) REVERT: K 322 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8132 (tt0) REVERT: K 324 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7676 (tttm) REVERT: K 346 GLN cc_start: 0.8389 (tp40) cc_final: 0.8048 (tt0) REVERT: A 95 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (m-40) REVERT: A 136 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5664 (mpp) REVERT: B 256 MET cc_start: 0.7378 (mtm) cc_final: 0.6542 (mmt) REVERT: B 292 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6486 (mttm) REVERT: B 324 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7421 (ttpp) REVERT: B 348 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8229 (mtt180) REVERT: B 359 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7311 (ttp-170) REVERT: B 404 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 461 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5528 (pp30) REVERT: C 63 MET cc_start: 0.8819 (mtt) cc_final: 0.8377 (mtt) REVERT: C 87 GLN cc_start: 0.7361 (mt0) cc_final: 0.6785 (mm110) REVERT: C 93 LYS cc_start: 0.8642 (mptt) cc_final: 0.8329 (mmtt) outliers start: 16 outliers final: 7 residues processed: 100 average time/residue: 0.1931 time to fit residues: 25.3222 Evaluate side-chains 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 A residue 136 MET Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLN 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 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 68 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6360 Z= 0.225 Angle : 0.598 7.518 8654 Z= 0.308 Chirality : 0.045 0.160 966 Planarity : 0.005 0.050 1111 Dihedral : 5.284 39.420 835 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.55 % Allowed : 10.76 % Favored : 86.69 % 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: -1.03 (0.30), residues: 772 helix: -0.24 (0.47), residues: 131 sheet: 0.97 (0.31), residues: 289 loop : -2.41 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 78 HIS 0.005 0.001 HIS B 439 PHE 0.016 0.001 PHE K 376 TYR 0.018 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 104 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7509 (m-80) cc_final: 0.7191 (m-80) REVERT: K 322 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8171 (tt0) REVERT: K 324 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7765 (tttm) REVERT: K 338 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6879 (mttm) REVERT: K 346 GLN cc_start: 0.8404 (tp40) cc_final: 0.8089 (tt0) REVERT: K 465 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8226 (pp) REVERT: A 95 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (m-40) REVERT: A 136 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5594 (mpp) REVERT: B 256 MET cc_start: 0.7373 (mtm) cc_final: 0.6494 (mmt) REVERT: B 292 LYS cc_start: 0.7406 (ttmt) cc_final: 0.6623 (mttm) REVERT: B 324 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7042 (tptt) REVERT: B 348 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8236 (mtt180) REVERT: B 359 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7361 (ttp-170) REVERT: B 404 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 461 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5517 (pp30) REVERT: C 87 GLN cc_start: 0.7374 (mt0) cc_final: 0.6763 (mm110) REVERT: C 93 LYS cc_start: 0.8647 (mptt) cc_final: 0.8330 (mmtt) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.1848 time to fit residues: 23.3491 Evaluate side-chains 99 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 322 GLU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 GLN 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 169 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2689 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= 0.205 Angle : 0.577 7.147 8654 Z= 0.297 Chirality : 0.044 0.160 966 Planarity : 0.005 0.051 1111 Dihedral : 5.091 39.120 835 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.12 % Allowed : 11.05 % Favored : 85.84 % 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: -0.82 (0.30), residues: 772 helix: -0.07 (0.47), residues: 131 sheet: 1.11 (0.31), residues: 289 loop : -2.30 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 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 109 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.744 Fit side-chains REVERT: K 282 TYR cc_start: 0.7514 (m-80) cc_final: 0.7256 (m-80) REVERT: K 287 GLU cc_start: 0.6710 (tt0) cc_final: 0.6277 (pp20) REVERT: K 322 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8107 (tt0) REVERT: K 324 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7773 (tttm) REVERT: K 338 LYS cc_start: 0.7224 (mmtt) cc_final: 0.6972 (mttm) REVERT: K 462 ASP cc_start: 0.7730 (p0) cc_final: 0.6964 (t0) REVERT: K 465 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 95 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (m-40) REVERT: A 112 ASN cc_start: 0.8176 (m-40) cc_final: 0.7370 (p0) REVERT: A 136 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5721 (mpp) REVERT: B 256 MET cc_start: 0.7357 (mtm) cc_final: 0.6472 (mmt) REVERT: B 292 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6877 (mttm) REVERT: B 324 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7050 (tptt) REVERT: B 348 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8328 (mtt180) REVERT: B 404 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 461 GLN cc_start: 0.5930 (OUTLIER) cc_final: 0.5388 (pp30) REVERT: C 85 ASN cc_start: 0.7789 (m-40) cc_final: 0.7270 (p0) REVERT: C 87 GLN cc_start: 0.7375 (mt0) cc_final: 0.6748 (mm110) REVERT: C 93 LYS cc_start: 0.8652 (mptt) cc_final: 0.8336 (mmtt) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.1822 time to fit residues: 23.9476 Evaluate side-chains 102 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 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 95 ASN 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 454 GLU Chi-restraints excluded: chain B residue 461 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6360 Z= 0.251 Angle : 0.611 8.033 8654 Z= 0.316 Chirality : 0.045 0.164 966 Planarity : 0.005 0.049 1111 Dihedral : 5.195 45.116 835 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.12 % Allowed : 11.19 % 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: -0.72 (0.30), residues: 772 helix: -0.00 (0.47), residues: 132 sheet: 1.15 (0.31), residues: 290 loop : -2.20 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 78 HIS 0.005 0.001 HIS B 439 PHE 0.017 0.001 PHE K 376 TYR 0.019 0.001 TYR B 411 ARG 0.002 0.000 ARG A 126 *********************** 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 109 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.657 Fit side-chains REVERT: K 282 TYR cc_start: 0.7455 (m-80) cc_final: 0.6928 (m-80) REVERT: K 322 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8117 (tt0) REVERT: K 324 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7748 (tttm) REVERT: K 338 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6866 (mttm) REVERT: K 346 GLN cc_start: 0.8409 (tp40) cc_final: 0.8129 (tt0) REVERT: K 462 ASP cc_start: 0.7752 (p0) cc_final: 0.6914 (t0) REVERT: A 95 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8292 (m-40) REVERT: A 112 ASN cc_start: 0.8163 (m-40) cc_final: 0.7365 (p0) REVERT: A 136 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5747 (mpp) REVERT: B 256 MET cc_start: 0.7371 (mtm) cc_final: 0.6509 (mmt) REVERT: B 292 LYS cc_start: 0.7475 (ttmt) cc_final: 0.6899 (mttm) REVERT: B 324 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7390 (ttpp) REVERT: B 348 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8298 (mtt180) REVERT: B 404 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 461 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5548 (pp30) REVERT: C 87 GLN cc_start: 0.7365 (mt0) cc_final: 0.6734 (mm110) REVERT: C 93 LYS cc_start: 0.8654 (mptt) cc_final: 0.8334 (mmtt) outliers start: 22 outliers final: 16 residues processed: 102 average time/residue: 0.1864 time to fit residues: 25.1300 Evaluate side-chains 105 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 476 ILE 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 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 8 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 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 57 ASN B 365 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2833 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= 0.210 Angle : 0.581 7.182 8654 Z= 0.300 Chirality : 0.044 0.160 966 Planarity : 0.005 0.049 1111 Dihedral : 5.074 45.444 835 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 11.90 % Favored : 85.27 % 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: -0.62 (0.30), residues: 772 helix: 0.07 (0.47), residues: 132 sheet: 1.24 (0.31), residues: 289 loop : -2.15 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 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 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 106 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.632 Fit side-chains REVERT: K 322 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8105 (tt0) REVERT: K 324 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7640 (tttm) REVERT: K 338 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6779 (mttm) REVERT: K 346 GLN cc_start: 0.8399 (tp40) cc_final: 0.8122 (tt0) REVERT: K 462 ASP cc_start: 0.7673 (p0) cc_final: 0.6855 (t0) REVERT: A 95 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8274 (m-40) REVERT: A 112 ASN cc_start: 0.8150 (m-40) cc_final: 0.7355 (p0) REVERT: A 136 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5909 (mpp) REVERT: B 256 MET cc_start: 0.7320 (mtm) cc_final: 0.6419 (mmt) REVERT: B 292 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6950 (mttm) REVERT: B 348 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8301 (mtt180) REVERT: B 404 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 461 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.5206 (pp30) REVERT: C 85 ASN cc_start: 0.7889 (m-40) cc_final: 0.7254 (p0) REVERT: C 87 GLN cc_start: 0.7315 (mt0) cc_final: 0.6720 (mm110) REVERT: C 93 LYS cc_start: 0.8656 (mptt) cc_final: 0.8340 (mmtt) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.1924 time to fit residues: 24.8428 Evaluate side-chains 103 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2895 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= 0.222 Angle : 0.587 7.440 8654 Z= 0.303 Chirality : 0.044 0.161 966 Planarity : 0.005 0.046 1111 Dihedral : 5.065 45.367 835 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 11.90 % Favored : 85.27 % 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: -0.64 (0.30), residues: 772 helix: -0.13 (0.46), residues: 138 sheet: 1.28 (0.31), residues: 289 loop : -2.17 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 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 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 108 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.699 Fit side-chains REVERT: K 322 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8110 (tt0) REVERT: K 324 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7646 (tttm) REVERT: K 338 LYS cc_start: 0.7094 (mmtt) cc_final: 0.6765 (mttm) REVERT: K 346 GLN cc_start: 0.8375 (tp40) cc_final: 0.8111 (tt0) REVERT: K 462 ASP cc_start: 0.7681 (p0) cc_final: 0.6831 (t0) REVERT: A 95 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8295 (m-40) REVERT: A 112 ASN cc_start: 0.8130 (m-40) cc_final: 0.7355 (p0) REVERT: B 256 MET cc_start: 0.7332 (mtm) cc_final: 0.6440 (mmt) REVERT: B 292 LYS cc_start: 0.7479 (ttmt) cc_final: 0.6767 (mmtm) REVERT: B 348 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8308 (mtt180) REVERT: B 404 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 461 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.4437 (mp10) REVERT: C 85 ASN cc_start: 0.7892 (m-40) cc_final: 0.7247 (p0) REVERT: C 87 GLN cc_start: 0.7328 (mt0) cc_final: 0.6740 (mm110) REVERT: C 93 LYS cc_start: 0.8658 (mptt) cc_final: 0.8341 (mmtt) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.1796 time to fit residues: 24.1382 Evaluate side-chains 103 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 GLN 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 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 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6360 Z= 0.162 Angle : 0.541 6.696 8654 Z= 0.277 Chirality : 0.043 0.154 966 Planarity : 0.004 0.046 1111 Dihedral : 4.780 44.091 835 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 12.32 % Favored : 85.27 % 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: -0.51 (0.30), residues: 772 helix: -0.03 (0.46), residues: 137 sheet: 1.39 (0.31), residues: 288 loop : -2.09 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.003 0.001 HIS B 439 PHE 0.011 0.001 PHE B 409 TYR 0.013 0.001 TYR B 411 ARG 0.002 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 fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.724 Fit side-chains REVERT: K 322 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8105 (tt0) REVERT: K 324 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7646 (tttm) REVERT: K 338 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6824 (mttm) REVERT: A 95 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8260 (m-40) REVERT: A 97 ASN cc_start: 0.7766 (p0) cc_final: 0.7551 (p0) REVERT: A 112 ASN cc_start: 0.8109 (m-40) cc_final: 0.7340 (p0) REVERT: A 136 MET cc_start: 0.5910 (mmp) cc_final: 0.5619 (mpp) REVERT: B 256 MET cc_start: 0.7284 (mtm) cc_final: 0.6388 (mmt) REVERT: B 292 LYS cc_start: 0.7388 (ttmt) cc_final: 0.6639 (mmtm) REVERT: C 85 ASN cc_start: 0.7891 (m-40) cc_final: 0.7243 (p0) REVERT: C 87 GLN cc_start: 0.7326 (mt0) cc_final: 0.6732 (mm110) REVERT: C 93 LYS cc_start: 0.8676 (mptt) cc_final: 0.8347 (mmtt) REVERT: C 134 GLN cc_start: 0.8020 (tt0) cc_final: 0.7592 (tt0) outliers start: 17 outliers final: 15 residues processed: 95 average time/residue: 0.1838 time to fit residues: 23.1473 Evaluate side-chains 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6360 Z= 0.180 Angle : 0.559 6.635 8654 Z= 0.288 Chirality : 0.043 0.155 966 Planarity : 0.004 0.046 1111 Dihedral : 4.756 44.712 835 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 12.61 % Favored : 84.99 % 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: -0.38 (0.31), residues: 772 helix: 0.07 (0.45), residues: 138 sheet: 1.44 (0.31), residues: 289 loop : -1.99 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.003 0.001 HIS B 439 PHE 0.012 0.001 PHE K 376 TYR 0.014 0.001 TYR B 411 ARG 0.002 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 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.700 Fit side-chains REVERT: K 322 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8101 (tt0) REVERT: K 324 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7651 (tttm) REVERT: K 462 ASP cc_start: 0.7770 (p0) cc_final: 0.6803 (t0) REVERT: A 95 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8265 (m-40) REVERT: A 97 ASN cc_start: 0.7764 (p0) cc_final: 0.7552 (p0) REVERT: A 112 ASN cc_start: 0.8117 (m-40) cc_final: 0.7335 (p0) REVERT: B 256 MET cc_start: 0.7322 (mtm) cc_final: 0.6462 (mmt) REVERT: B 292 LYS cc_start: 0.7367 (ttmt) cc_final: 0.6622 (mmtm) REVERT: C 87 GLN cc_start: 0.7326 (mt0) cc_final: 0.6729 (mm110) REVERT: C 93 LYS cc_start: 0.8680 (mptt) cc_final: 0.8351 (mmtt) REVERT: C 134 GLN cc_start: 0.8031 (tt0) cc_final: 0.7587 (tt0) outliers start: 17 outliers final: 16 residues processed: 94 average time/residue: 0.1795 time to fit residues: 22.6163 Evaluate side-chains 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 454 GLU Chi-restraints excluded: chain B residue 476 ILE 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 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: 0.6980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 43 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.189434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.110644 restraints weight = 6915.616| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.18 r_work: 0.2943 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6360 Z= 0.181 Angle : 0.557 6.753 8654 Z= 0.286 Chirality : 0.043 0.156 966 Planarity : 0.004 0.044 1111 Dihedral : 4.763 44.575 835 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.41 % Allowed : 12.61 % Favored : 84.99 % 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: -0.34 (0.31), residues: 772 helix: 0.18 (0.45), residues: 137 sheet: 1.37 (0.31), residues: 293 loop : -1.94 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 281 HIS 0.003 0.001 HIS B 439 PHE 0.012 0.001 PHE K 376 TYR 0.014 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: 1642.69 seconds wall clock time: 30 minutes 37.23 seconds (1837.23 seconds total)