Starting phenix.real_space_refine on Mon Mar 11 00:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/03_2024/7wso_32762.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/03_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_32762/03_2024/7wso_32762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/03_2024/7wso_32762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/03_2024/7wso_32762.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wso_32762/03_2024/7wso_32762.pdb" } 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 Residue "K PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.10, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 2.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.93 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: 2.30 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: 97.59 - 105.74: 188 105.74 - 113.89: 3565 113.89 - 122.04: 3528 122.04 - 130.19: 1314 130.19 - 138.34: 59 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 2.520 nonbonded pdb=" O MET C 163 " pdb=" OG1 THR C 166 " model vdw 2.388 2.440 nonbonded pdb=" O SER K 486 " pdb=" OG1 THR K 490 " model vdw 2.397 2.440 nonbonded pdb=" O GLN K 315 " pdb=" ND2 ASN K 319 " model vdw 2.417 2.520 nonbonded pdb=" OH TYR K 440 " pdb=" NE2 GLN K 442 " model vdw 2.427 2.520 ... (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 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: 1.130 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: 3.900 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.210 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- 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 : 0.849 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: 0.2211 time to fit residues: 37.6421 Evaluate side-chains 95 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 117 GLN A 127 GLN B 272 HIS B 319 ASN B 329 ASN B 394 ASN B 425 ASN B 439 HIS C 48 GLN C 68 ASN C 165 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1887 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= 0.205 Angle : 0.640 8.351 8654 Z= 0.333 Chirality : 0.045 0.160 966 Planarity : 0.006 0.060 1111 Dihedral : 5.848 45.450 837 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.12 % Allowed : 7.22 % Favored : 90.65 % 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: -1.80 (0.29), residues: 772 helix: -1.30 (0.44), residues: 130 sheet: 0.53 (0.32), residues: 282 loop : -2.69 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS K 439 PHE 0.014 0.001 PHE K 376 TYR 0.019 0.002 TYR B 411 ARG 0.002 0.000 ARG C 113 *********************** 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 112 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7501 (m-80) cc_final: 0.7083 (m-80) REVERT: K 316 ASP cc_start: 0.7827 (m-30) cc_final: 0.7456 (m-30) REVERT: K 322 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8075 (tt0) REVERT: K 324 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7620 (tttm) REVERT: K 341 SER cc_start: 0.9019 (p) cc_final: 0.8744 (t) REVERT: A 116 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7910 (mt0) REVERT: A 136 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5815 (pmt) REVERT: B 256 MET cc_start: 0.7400 (mtm) cc_final: 0.6591 (mmt) REVERT: B 292 LYS cc_start: 0.7415 (ttmt) cc_final: 0.6618 (mttm) REVERT: B 324 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7378 (ttpp) REVERT: B 348 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8221 (mtt180) REVERT: C 87 GLN cc_start: 0.7430 (mt0) cc_final: 0.6890 (mm110) REVERT: C 93 LYS cc_start: 0.8561 (mptt) cc_final: 0.8257 (mmtt) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.2104 time to fit residues: 28.7610 Evaluate side-chains 94 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 166 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: 0.8980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS B 365 ASN C 68 ASN C 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2393 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= 0.194 Angle : 0.582 7.275 8654 Z= 0.299 Chirality : 0.044 0.157 966 Planarity : 0.005 0.051 1111 Dihedral : 5.326 43.989 835 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.41 % Allowed : 9.49 % Favored : 88.10 % 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: -0.49 (0.46), residues: 130 sheet: 0.81 (0.31), residues: 287 loop : -2.50 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 469 HIS 0.004 0.001 HIS B 439 PHE 0.013 0.001 PHE K 376 TYR 0.015 0.001 TYR B 411 ARG 0.001 0.000 ARG A 126 *********************** 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 105 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7513 (m-80) cc_final: 0.7128 (m-80) REVERT: K 322 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8019 (tt0) REVERT: K 324 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7680 (tttm) REVERT: K 341 SER cc_start: 0.8901 (p) cc_final: 0.8693 (t) REVERT: K 346 GLN cc_start: 0.8386 (tp40) cc_final: 0.8047 (tt0) REVERT: A 95 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (m-40) REVERT: A 136 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5469 (pmt) REVERT: B 256 MET cc_start: 0.7340 (mtm) cc_final: 0.6502 (mmt) REVERT: B 292 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6493 (mttm) REVERT: B 324 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7416 (ttpp) REVERT: B 348 ARG cc_start: 0.8475 (mtt90) cc_final: 0.8228 (mtt180) REVERT: B 404 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 454 GLU cc_start: 0.6586 (tt0) cc_final: 0.5912 (pm20) REVERT: B 461 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5409 (pp30) REVERT: C 87 GLN cc_start: 0.7367 (mt0) cc_final: 0.6782 (mm110) REVERT: C 93 LYS cc_start: 0.8618 (mptt) cc_final: 0.8308 (mmtt) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 0.2088 time to fit residues: 26.9978 Evaluate side-chains 96 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 140 THR 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 49 SER Chi-restraints excluded: chain C residue 67 MET 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: 3.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 319 ASN B 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2535 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= 0.225 Angle : 0.597 7.757 8654 Z= 0.307 Chirality : 0.045 0.160 966 Planarity : 0.005 0.049 1111 Dihedral : 5.257 38.560 835 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.41 % Allowed : 11.05 % Favored : 86.54 % 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: -0.96 (0.30), residues: 772 helix: -0.12 (0.48), residues: 131 sheet: 1.02 (0.31), residues: 287 loop : -2.38 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 34 HIS 0.005 0.001 HIS B 439 PHE 0.015 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.001 0.000 ARG B 359 *********************** 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 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7509 (m-80) cc_final: 0.7203 (m-80) REVERT: K 322 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8123 (tt0) REVERT: K 324 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7753 (tttm) REVERT: K 338 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6817 (mttm) REVERT: K 465 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8175 (pp) REVERT: A 95 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: A 136 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5307 (mpp) REVERT: B 256 MET cc_start: 0.7405 (mtm) cc_final: 0.6539 (mmt) REVERT: B 292 LYS cc_start: 0.7406 (ttmt) cc_final: 0.6633 (mttm) REVERT: B 324 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7089 (tptt) REVERT: B 404 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 454 GLU cc_start: 0.6909 (tt0) cc_final: 0.5834 (pm20) REVERT: B 461 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5579 (pp30) REVERT: C 87 GLN cc_start: 0.7382 (mt0) cc_final: 0.6759 (mm110) REVERT: C 93 LYS cc_start: 0.8623 (mptt) cc_final: 0.8307 (mmtt) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 0.2188 time to fit residues: 26.9085 Evaluate side-chains 93 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 140 THR 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 C residue 49 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7747 moved from start: 0.2759 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= 0.184 Angle : 0.552 6.851 8654 Z= 0.283 Chirality : 0.043 0.156 966 Planarity : 0.005 0.050 1111 Dihedral : 4.964 37.661 835 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.27 % Allowed : 12.04 % 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: -0.74 (0.30), residues: 772 helix: 0.07 (0.48), residues: 131 sheet: 1.14 (0.31), residues: 289 loop : -2.24 (0.30), residues: 352 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 0.013 0.001 PHE K 376 TYR 0.015 0.001 TYR B 411 ARG 0.001 0.000 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 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.859 Fit side-chains REVERT: K 282 TYR cc_start: 0.7464 (m-80) cc_final: 0.7211 (m-80) REVERT: K 287 GLU cc_start: 0.6717 (tt0) cc_final: 0.6252 (pp20) REVERT: K 322 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8007 (tt0) REVERT: K 324 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7806 (tttm) REVERT: K 338 LYS cc_start: 0.7080 (mmtt) cc_final: 0.6776 (mttm) REVERT: K 465 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 43 MET cc_start: 0.8474 (mtp) cc_final: 0.8223 (mtm) REVERT: A 95 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8171 (m-40) REVERT: A 112 ASN cc_start: 0.8146 (m-40) cc_final: 0.7337 (p0) REVERT: A 136 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5671 (mpp) REVERT: B 256 MET cc_start: 0.7338 (mtm) cc_final: 0.6460 (mmt) REVERT: B 292 LYS cc_start: 0.7383 (ttmt) cc_final: 0.6803 (mttm) REVERT: B 324 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7062 (tptt) REVERT: B 404 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 454 GLU cc_start: 0.6782 (tt0) cc_final: 0.5856 (pm20) REVERT: C 85 ASN cc_start: 0.7787 (m-40) cc_final: 0.7269 (p0) REVERT: C 87 GLN cc_start: 0.7367 (mt0) cc_final: 0.6743 (mm110) REVERT: C 93 LYS cc_start: 0.8627 (mptt) cc_final: 0.8304 (mmtt) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1974 time to fit residues: 24.4373 Evaluate side-chains 94 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 140 THR 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 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 319 ASN B 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2769 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= 0.224 Angle : 0.584 7.680 8654 Z= 0.301 Chirality : 0.044 0.160 966 Planarity : 0.005 0.049 1111 Dihedral : 5.048 44.270 835 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.27 % Allowed : 12.04 % 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: -0.62 (0.30), residues: 772 helix: 0.18 (0.48), residues: 131 sheet: 1.21 (0.31), residues: 289 loop : -2.16 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 34 HIS 0.004 0.001 HIS B 439 PHE 0.015 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.001 0.000 ARG B 359 *********************** 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 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.794 Fit side-chains REVERT: K 282 TYR cc_start: 0.7520 (m-80) cc_final: 0.6970 (m-80) REVERT: K 322 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8083 (tt0) REVERT: K 324 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7806 (tttm) REVERT: A 43 MET cc_start: 0.8528 (mtp) cc_final: 0.8247 (mtm) REVERT: A 95 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: A 112 ASN cc_start: 0.8168 (m-40) cc_final: 0.7370 (p0) REVERT: A 136 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5955 (mmp) REVERT: B 256 MET cc_start: 0.7343 (mtm) cc_final: 0.6450 (mmt) REVERT: B 292 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6862 (mttm) REVERT: B 324 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7444 (ttpp) REVERT: B 454 GLU cc_start: 0.6922 (tt0) cc_final: 0.5880 (pm20) REVERT: B 476 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (mt) REVERT: C 87 GLN cc_start: 0.7341 (mt0) cc_final: 0.6715 (mm110) REVERT: C 93 LYS cc_start: 0.8630 (mptt) cc_final: 0.8307 (mmtt) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.1858 time to fit residues: 23.2773 Evaluate side-chains 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 140 THR 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 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN C 68 ASN ** 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: 0.7775 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6360 Z= 0.231 Angle : 0.582 7.539 8654 Z= 0.301 Chirality : 0.044 0.160 966 Planarity : 0.005 0.048 1111 Dihedral : 5.075 47.078 835 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.41 % Allowed : 12.46 % Favored : 85.13 % 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: 0.20 (0.47), residues: 131 sheet: 1.21 (0.31), residues: 289 loop : -2.15 (0.30), residues: 352 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 0.015 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.001 0.000 ARG C 57 *********************** 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 101 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.885 Fit side-chains REVERT: K 322 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8079 (tt0) REVERT: K 324 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7624 (tttm) REVERT: A 43 MET cc_start: 0.8538 (mtp) cc_final: 0.8245 (mtm) REVERT: A 95 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: A 112 ASN cc_start: 0.8138 (m-40) cc_final: 0.7358 (p0) REVERT: B 256 MET cc_start: 0.7322 (mtm) cc_final: 0.6425 (mmt) REVERT: B 292 LYS cc_start: 0.7491 (ttmt) cc_final: 0.6962 (mttm) REVERT: B 324 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7441 (ttpp) REVERT: B 454 GLU cc_start: 0.6965 (tt0) cc_final: 0.5853 (pm20) REVERT: B 476 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 68 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (p0) REVERT: C 87 GLN cc_start: 0.7311 (mt0) cc_final: 0.6710 (mm110) REVERT: C 93 LYS cc_start: 0.8635 (mptt) cc_final: 0.8316 (mmtt) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.2137 time to fit residues: 26.4301 Evaluate side-chains 99 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 381 ILE Chi-restraints excluded: chain B residue 404 SER 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 68 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.0040 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 127 GLN B 365 ASN C 68 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6360 Z= 0.230 Angle : 0.583 7.581 8654 Z= 0.301 Chirality : 0.044 0.160 966 Planarity : 0.005 0.047 1111 Dihedral : 5.067 46.247 835 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -0.66 (0.30), residues: 772 helix: -0.06 (0.45), residues: 142 sheet: 1.24 (0.31), residues: 289 loop : -2.21 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.005 0.001 HIS B 439 PHE 0.015 0.001 PHE K 376 TYR 0.017 0.001 TYR B 411 ARG 0.001 0.000 ARG A 124 *********************** 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 103 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.717 Fit side-chains REVERT: K 322 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8079 (tt0) REVERT: K 324 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7633 (tttm) REVERT: K 346 GLN cc_start: 0.8390 (tp40) cc_final: 0.8126 (tt0) REVERT: A 43 MET cc_start: 0.8532 (mtp) cc_final: 0.8231 (mtm) REVERT: A 95 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: A 112 ASN cc_start: 0.8127 (m-40) cc_final: 0.7355 (p0) REVERT: B 256 MET cc_start: 0.7293 (mtm) cc_final: 0.6408 (mmt) REVERT: B 292 LYS cc_start: 0.7493 (ttmt) cc_final: 0.6755 (mmtm) REVERT: B 324 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7453 (ttpp) REVERT: B 454 GLU cc_start: 0.6987 (tt0) cc_final: 0.5896 (pm20) REVERT: B 476 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8038 (mt) REVERT: C 87 GLN cc_start: 0.7337 (mt0) cc_final: 0.6742 (mm110) REVERT: C 93 LYS cc_start: 0.8635 (mptt) cc_final: 0.8316 (mmtt) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1904 time to fit residues: 24.2200 Evaluate side-chains 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 142 ASN 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 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.3000 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= 0.211 Angle : 0.570 7.233 8654 Z= 0.294 Chirality : 0.044 0.159 966 Planarity : 0.005 0.047 1111 Dihedral : 4.992 46.068 835 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.55 % Allowed : 12.46 % 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: -0.54 (0.30), residues: 772 helix: 0.07 (0.46), residues: 142 sheet: 1.30 (0.31), residues: 289 loop : -2.15 (0.30), residues: 341 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 0.014 0.001 PHE K 376 TYR 0.016 0.001 TYR B 411 ARG 0.001 0.000 ARG K 348 *********************** 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 100 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.787 Fit side-chains REVERT: K 322 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8088 (tt0) REVERT: K 324 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7595 (tttm) REVERT: K 346 GLN cc_start: 0.8374 (tp40) cc_final: 0.8112 (tt0) REVERT: A 43 MET cc_start: 0.8534 (mtp) cc_final: 0.8231 (mtm) REVERT: A 95 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: A 112 ASN cc_start: 0.8125 (m-40) cc_final: 0.7343 (p0) REVERT: A 138 GLU cc_start: 0.8205 (tp30) cc_final: 0.7723 (tp30) REVERT: B 256 MET cc_start: 0.7285 (mtm) cc_final: 0.6394 (mmt) REVERT: B 292 LYS cc_start: 0.7482 (ttmt) cc_final: 0.6728 (mmtm) REVERT: B 324 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7470 (ttpp) REVERT: B 404 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 454 GLU cc_start: 0.6937 (tt0) cc_final: 0.5879 (pm20) REVERT: C 87 GLN cc_start: 0.7333 (mt0) cc_final: 0.6738 (mm110) REVERT: C 93 LYS cc_start: 0.8637 (mptt) cc_final: 0.8318 (mmtt) outliers start: 18 outliers final: 14 residues processed: 96 average time/residue: 0.1950 time to fit residues: 24.6652 Evaluate side-chains 96 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 142 ASN 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 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 147 THR Chi-restraints excluded: chain C residue 168 LEU 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: 0.1980 chunk 6 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- 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: 0.7734 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 : 0.002 0.029 6360 Z= 0.154 Angle : 0.526 6.363 8654 Z= 0.268 Chirality : 0.042 0.152 966 Planarity : 0.004 0.047 1111 Dihedral : 4.659 45.137 835 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.12 % Allowed : 12.75 % Favored : 85.13 % 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: -0.35 (0.31), residues: 772 helix: 0.25 (0.46), residues: 141 sheet: 1.35 (0.31), residues: 294 loop : -2.01 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 281 HIS 0.002 0.001 HIS B 439 PHE 0.011 0.001 PHE B 409 TYR 0.013 0.001 TYR B 411 ARG 0.001 0.000 ARG K 348 ********************** 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: 15 poor density : 85 time to evaluate : 0.684 Fit side-chains REVERT: K 322 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8086 (tt0) REVERT: K 324 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7592 (tttm) REVERT: A 95 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8174 (m-40) REVERT: A 112 ASN cc_start: 0.8102 (m-40) cc_final: 0.7339 (p0) REVERT: B 256 MET cc_start: 0.7247 (mtm) cc_final: 0.6375 (mmt) REVERT: B 292 LYS cc_start: 0.7378 (ttmt) cc_final: 0.6643 (mmtm) REVERT: B 324 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7405 (ttpp) REVERT: B 454 GLU cc_start: 0.6425 (tt0) cc_final: 0.5707 (pm20) REVERT: B 476 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8082 (mt) REVERT: C 87 GLN cc_start: 0.7275 (mt0) cc_final: 0.6687 (mm110) REVERT: C 93 LYS cc_start: 0.8674 (mptt) cc_final: 0.8338 (mmtt) REVERT: C 134 GLN cc_start: 0.8054 (tt0) cc_final: 0.7829 (tt0) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.1884 time to fit residues: 23.4575 Evaluate side-chains 95 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU 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 140 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.187161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106508 restraints weight = 6926.507| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.80 r_work: 0.2923 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6360 Z= 0.320 Angle : 0.644 8.881 8654 Z= 0.333 Chirality : 0.046 0.166 966 Planarity : 0.005 0.045 1111 Dihedral : 5.228 46.658 835 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.41 % Allowed : 12.46 % Favored : 85.13 % 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: 0.24 (0.46), residues: 142 sheet: 1.42 (0.31), residues: 281 loop : -2.06 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 281 HIS 0.007 0.001 HIS B 439 PHE 0.020 0.002 PHE K 376 TYR 0.019 0.002 TYR B 411 ARG 0.002 0.000 ARG C 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.02 seconds wall clock time: 34 minutes 1.44 seconds (2041.44 seconds total)