Starting phenix.real_space_refine on Tue Feb 11 20:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrh_21368/02_2025/6vrh_21368.cif" } resolution = 3.3 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= -0.001 sd= 0.946 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' CL': 1, '8PR': 1, 'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.18, per 1000 atoms: 0.84 Number of scatterers: 6142 At special positions: 0 Unit cell: (96.552, 103.032, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 F 1 9.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 704 " - " ASN A 217 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 953.4 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 57.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.752A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.525A pdb=" N ALA A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.858A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.639A pdb=" N ARG A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.250A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.653A pdb=" N THR A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.701A pdb=" N ARG A 241 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.591A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.155A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.698A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 4.354A pdb=" N GLY A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.546A pdb=" N LEU A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.248A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.565A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.688A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.631A pdb=" N VAL A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 419 through 454 removed outlier: 3.694A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.657A pdb=" N VAL A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.758A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.777A pdb=" N SER A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.045A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.546A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 removed outlier: 3.740A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.931A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.877A pdb=" N LYS B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.553A pdb=" N THR C 89 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N GLN C 47 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N SER C 87 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N VAL C 49 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N SER C 85 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.052A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 127 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 897 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: 1.58 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1812 1.34 - 1.46: 1621 1.46 - 1.58: 2844 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 1.509 1.570 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CAV 8PR A 702 " pdb=" OAQ 8PR A 702 " ideal model delta sigma weight residual 1.354 1.413 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" CAI 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.452 1.504 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" CAU 8PR A 702 " pdb=" OAP 8PR A 702 " ideal model delta sigma weight residual 1.362 1.413 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAK 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.451 1.498 -0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8515 2.20 - 4.40: 80 4.40 - 6.60: 16 6.60 - 8.80: 6 8.80 - 11.00: 2 Bond angle restraints: 8619 Sorted by residual: angle pdb=" CAE 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 120.67 109.67 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C2 LMT A 705 " pdb=" C3 LMT A 705 " pdb=" C4 LMT A 705 " ideal model delta sigma weight residual 117.09 107.26 9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAF 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 121.28 130.08 -8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C10 LMT A 705 " pdb=" C9 LMT A 705 " pdb=" C8 LMT A 705 " ideal model delta sigma weight residual 116.03 107.37 8.66 3.00e+00 1.11e-01 8.33e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 3574 29.14 - 58.27: 111 58.27 - 87.41: 2 87.41 - 116.54: 1 116.54 - 145.68: 1 Dihedral angle restraints: 3689 sinusoidal: 1475 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 129.71 50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CAX 8PR A 702 " pdb=" CAM 8PR A 702 " pdb=" CAW 8PR A 702 " pdb=" OAO 8PR A 702 " ideal model delta sinusoidal sigma weight residual 182.60 36.92 145.68 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 727 0.043 - 0.085: 193 0.085 - 0.128: 41 0.128 - 0.171: 1 0.171 - 0.213: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 705 " pdb=" C4' LMT A 705 " pdb=" C6' LMT A 705 " pdb=" O5' LMT A 705 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C4' LMT A 705 " pdb=" C3' LMT A 705 " pdb=" C5' LMT A 705 " pdb=" O1B LMT A 705 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CAX 8PR A 702 " pdb=" CAJ 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAW 8PR A 702 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 122 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.21e+00 pdb=" N PRO A 288 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 743 2.75 - 3.29: 6254 3.29 - 3.82: 10369 3.82 - 4.36: 11887 4.36 - 4.90: 20868 Nonbonded interactions: 50121 Sorted by model distance: nonbonded pdb=" O PRO A 571 " pdb=" OG SER A 574 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 242 " pdb=" O LEU A 248 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLN C 109 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 328 " pdb=" O4' LMT A 705 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 83 " pdb=" OG1 THR C 94 " model vdw 2.307 3.040 ... (remaining 50116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.004 0.061 6326 Z= 0.251 Angle : 0.604 11.004 8619 Z= 0.292 Chirality : 0.040 0.213 966 Planarity : 0.004 0.073 1048 Dihedral : 13.500 145.676 2274 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.27), residues: 758 helix: -1.15 (0.24), residues: 360 sheet: -2.83 (0.43), residues: 105 loop : -2.61 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.006 0.001 HIS C 111 PHE 0.013 0.001 PHE A 380 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7829 (t80) cc_final: 0.7608 (t80) REVERT: A 270 ILE cc_start: 0.7191 (tp) cc_final: 0.6813 (tp) REVERT: A 271 TRP cc_start: 0.5986 (p-90) cc_final: 0.5554 (p-90) REVERT: A 272 LYS cc_start: 0.8402 (tppp) cc_final: 0.7912 (tptt) REVERT: A 311 PHE cc_start: 0.6600 (m-10) cc_final: 0.6390 (m-80) REVERT: A 316 ASN cc_start: 0.7477 (t0) cc_final: 0.6860 (t0) REVERT: A 615 GLU cc_start: 0.5133 (mp0) cc_final: 0.3315 (pt0) REVERT: C 62 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6364 (mt0) REVERT: C 73 TYR cc_start: 0.8083 (m-80) cc_final: 0.7785 (m-80) REVERT: C 81 ARG cc_start: 0.6620 (tpm170) cc_final: 0.4840 (ptt90) REVERT: C 123 LYS cc_start: 0.6894 (mptt) cc_final: 0.6315 (mtpt) REVERT: B 39 ILE cc_start: 0.6117 (mm) cc_final: 0.5844 (tp) REVERT: B 57 LYS cc_start: 0.7771 (tttt) cc_final: 0.7131 (tttt) REVERT: B 130 GLN cc_start: 0.7601 (pt0) cc_final: 0.7401 (pt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1907 time to fit residues: 27.8009 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 111 GLN A 112 ASN A 235 HIS C 26 GLN C 47 GLN C 57 GLN B 54 ASN B 69 ASN B 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.198988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178818 restraints weight = 7969.329| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.84 r_work: 0.3828 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.193 Angle : 0.544 8.562 8619 Z= 0.281 Chirality : 0.039 0.143 966 Planarity : 0.004 0.078 1048 Dihedral : 7.837 128.083 958 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.54 % Allowed : 10.92 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.30), residues: 758 helix: 0.21 (0.26), residues: 369 sheet: -2.19 (0.44), residues: 106 loop : -2.11 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.009 0.001 HIS C 111 PHE 0.017 0.001 PHE A 548 TYR 0.034 0.002 TYR A 142 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8073 (t80) cc_final: 0.7764 (t80) REVERT: A 204 TRP cc_start: 0.6741 (p90) cc_final: 0.6152 (p90) REVERT: A 270 ILE cc_start: 0.6911 (tp) cc_final: 0.6598 (tp) REVERT: A 271 TRP cc_start: 0.5777 (p-90) cc_final: 0.5277 (p-90) REVERT: A 272 LYS cc_start: 0.8538 (tppp) cc_final: 0.8030 (tptp) REVERT: A 316 ASN cc_start: 0.7427 (t0) cc_final: 0.6763 (t0) REVERT: A 615 GLU cc_start: 0.5208 (mp0) cc_final: 0.3176 (pt0) REVERT: C 56 TYR cc_start: 0.8649 (m-80) cc_final: 0.8188 (m-80) REVERT: C 62 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6373 (mt0) REVERT: C 81 ARG cc_start: 0.6863 (tpm170) cc_final: 0.5010 (ptt90) REVERT: C 123 LYS cc_start: 0.7095 (mptt) cc_final: 0.6357 (mtpt) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.1762 time to fit residues: 20.2182 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.197520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176387 restraints weight = 8039.500| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.03 r_work: 0.3929 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6326 Z= 0.212 Angle : 0.542 7.922 8619 Z= 0.282 Chirality : 0.040 0.147 966 Planarity : 0.004 0.079 1048 Dihedral : 7.212 117.717 958 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.62 % Allowed : 12.62 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 758 helix: 0.62 (0.27), residues: 373 sheet: -1.75 (0.46), residues: 106 loop : -1.92 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.010 0.001 HIS C 111 PHE 0.030 0.001 PHE A 311 TYR 0.022 0.001 TYR A 142 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8169 (t80) cc_final: 0.7839 (t80) REVERT: A 204 TRP cc_start: 0.6783 (p90) cc_final: 0.6260 (p90) REVERT: A 270 ILE cc_start: 0.6892 (tp) cc_final: 0.6555 (tp) REVERT: A 316 ASN cc_start: 0.7449 (t0) cc_final: 0.6754 (t0) REVERT: A 507 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6792 (tt) REVERT: A 615 GLU cc_start: 0.5229 (mp0) cc_final: 0.4891 (mm-30) REVERT: C 56 TYR cc_start: 0.8739 (m-80) cc_final: 0.8161 (m-80) REVERT: C 62 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6363 (mt0) REVERT: C 81 ARG cc_start: 0.6910 (tpm170) cc_final: 0.5119 (ptt90) REVERT: C 123 LYS cc_start: 0.7130 (mptt) cc_final: 0.6381 (mtpt) REVERT: B 54 ASN cc_start: 0.8276 (m110) cc_final: 0.7951 (m-40) outliers start: 17 outliers final: 12 residues processed: 89 average time/residue: 0.1794 time to fit residues: 21.7948 Evaluate side-chains 89 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.197421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176238 restraints weight = 8038.789| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.06 r_work: 0.3944 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6326 Z= 0.163 Angle : 0.512 7.765 8619 Z= 0.266 Chirality : 0.039 0.141 966 Planarity : 0.004 0.077 1048 Dihedral : 6.461 102.173 958 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.00 % Allowed : 15.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.31), residues: 758 helix: 0.88 (0.27), residues: 373 sheet: -1.33 (0.47), residues: 106 loop : -1.70 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 PHE 0.044 0.001 PHE A 311 TYR 0.022 0.001 TYR A 134 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.663 Fit side-chains REVERT: A 176 TYR cc_start: 0.8130 (t80) cc_final: 0.7857 (t80) REVERT: A 204 TRP cc_start: 0.6773 (p90) cc_final: 0.6222 (p90) REVERT: A 241 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7487 (mtp180) REVERT: A 270 ILE cc_start: 0.6869 (tp) cc_final: 0.6536 (tp) REVERT: A 271 TRP cc_start: 0.5761 (p-90) cc_final: 0.5333 (p-90) REVERT: A 316 ASN cc_start: 0.7396 (t0) cc_final: 0.6690 (t0) REVERT: A 606 GLU cc_start: 0.6384 (tt0) cc_final: 0.6121 (tt0) REVERT: A 615 GLU cc_start: 0.5279 (mp0) cc_final: 0.4928 (mm-30) REVERT: C 31 MET cc_start: 0.1768 (mtm) cc_final: 0.1481 (mpp) REVERT: C 62 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6396 (mt0) REVERT: C 73 TYR cc_start: 0.7860 (m-80) cc_final: 0.7586 (m-80) REVERT: C 81 ARG cc_start: 0.7004 (tpm170) cc_final: 0.5150 (ptt90) REVERT: C 123 LYS cc_start: 0.7133 (mptt) cc_final: 0.6363 (tttm) REVERT: B 54 ASN cc_start: 0.7867 (m110) cc_final: 0.7312 (m-40) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.1942 time to fit residues: 22.7368 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.198921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177724 restraints weight = 7991.075| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.04 r_work: 0.3939 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.175 Angle : 0.512 7.799 8619 Z= 0.267 Chirality : 0.039 0.135 966 Planarity : 0.004 0.077 1048 Dihedral : 6.034 85.831 958 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.31 % Allowed : 16.31 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 758 helix: 0.96 (0.27), residues: 376 sheet: -1.20 (0.47), residues: 106 loop : -1.48 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 PHE 0.036 0.001 PHE A 311 TYR 0.022 0.001 TYR A 134 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7529 (mmp) cc_final: 0.7186 (mmp) REVERT: A 135 MET cc_start: 0.8716 (ttp) cc_final: 0.8462 (ttp) REVERT: A 176 TYR cc_start: 0.8181 (t80) cc_final: 0.7932 (t80) REVERT: A 204 TRP cc_start: 0.6844 (p90) cc_final: 0.6292 (p90) REVERT: A 271 TRP cc_start: 0.5841 (p-90) cc_final: 0.5395 (p-90) REVERT: A 316 ASN cc_start: 0.7469 (t0) cc_final: 0.6747 (t0) REVERT: A 507 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6914 (tt) REVERT: A 606 GLU cc_start: 0.6286 (tt0) cc_final: 0.5996 (tt0) REVERT: A 615 GLU cc_start: 0.5404 (mp0) cc_final: 0.5007 (mm-30) REVERT: C 31 MET cc_start: 0.1778 (mtm) cc_final: 0.1484 (mpp) REVERT: C 62 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6480 (mt0) REVERT: C 81 ARG cc_start: 0.7015 (tpm170) cc_final: 0.5150 (ptt90) REVERT: C 123 LYS cc_start: 0.7148 (mptt) cc_final: 0.6413 (tttm) REVERT: B 54 ASN cc_start: 0.8059 (m110) cc_final: 0.7793 (m-40) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 0.1771 time to fit residues: 20.4400 Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.198967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177404 restraints weight = 7945.160| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.12 r_work: 0.3914 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6326 Z= 0.160 Angle : 0.501 7.834 8619 Z= 0.260 Chirality : 0.038 0.131 966 Planarity : 0.004 0.077 1048 Dihedral : 5.818 74.147 958 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.62 % Allowed : 17.54 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 758 helix: 1.12 (0.27), residues: 373 sheet: -1.08 (0.49), residues: 106 loop : -1.28 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 PHE 0.031 0.001 PHE A 311 TYR 0.018 0.001 TYR A 134 ARG 0.004 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.685 Fit side-chains REVERT: A 204 TRP cc_start: 0.7025 (p90) cc_final: 0.6371 (p90) REVERT: A 271 TRP cc_start: 0.6104 (p-90) cc_final: 0.5642 (p-90) REVERT: A 316 ASN cc_start: 0.7667 (t0) cc_final: 0.6974 (t0) REVERT: A 507 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 606 GLU cc_start: 0.6137 (tt0) cc_final: 0.5833 (tt0) REVERT: A 615 GLU cc_start: 0.5508 (mp0) cc_final: 0.5011 (mp0) REVERT: C 31 MET cc_start: 0.1821 (mtm) cc_final: 0.1565 (mpp) REVERT: C 62 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6729 (mt0) REVERT: C 81 ARG cc_start: 0.7138 (tpm170) cc_final: 0.5354 (ptt90) REVERT: C 123 LYS cc_start: 0.7219 (mptt) cc_final: 0.6588 (tttm) REVERT: B 46 TYR cc_start: 0.5931 (m-80) cc_final: 0.5666 (m-80) REVERT: B 54 ASN cc_start: 0.7903 (m110) cc_final: 0.7628 (m-40) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.1668 time to fit residues: 19.6339 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175862 restraints weight = 7995.174| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.11 r_work: 0.3887 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.199 Angle : 0.532 7.920 8619 Z= 0.277 Chirality : 0.039 0.130 966 Planarity : 0.004 0.079 1048 Dihedral : 5.867 69.035 958 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.62 % Allowed : 18.31 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 758 helix: 0.96 (0.27), residues: 381 sheet: -0.95 (0.49), residues: 106 loop : -1.33 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.009 0.001 HIS C 111 PHE 0.033 0.001 PHE A 428 TYR 0.023 0.001 TYR A 176 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.633 Fit side-chains REVERT: A 204 TRP cc_start: 0.6981 (p90) cc_final: 0.6523 (p90) REVERT: A 271 TRP cc_start: 0.6082 (p-90) cc_final: 0.5660 (p-90) REVERT: A 316 ASN cc_start: 0.7684 (t0) cc_final: 0.6976 (t0) REVERT: A 507 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7123 (tt) REVERT: A 606 GLU cc_start: 0.6189 (tt0) cc_final: 0.5871 (tt0) REVERT: A 615 GLU cc_start: 0.5544 (mp0) cc_final: 0.4996 (mp0) REVERT: C 62 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6735 (mt0) REVERT: C 81 ARG cc_start: 0.7158 (tpm170) cc_final: 0.5340 (ptt90) REVERT: C 123 LYS cc_start: 0.7272 (mptt) cc_final: 0.6643 (tttm) REVERT: B 46 TYR cc_start: 0.5914 (m-80) cc_final: 0.5638 (m-80) REVERT: B 54 ASN cc_start: 0.8047 (m110) cc_final: 0.7792 (m-40) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.1600 time to fit residues: 19.5905 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178195 restraints weight = 7935.383| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.13 r_work: 0.3869 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6326 Z= 0.154 Angle : 0.517 7.730 8619 Z= 0.268 Chirality : 0.038 0.128 966 Planarity : 0.004 0.077 1048 Dihedral : 5.797 63.740 958 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.46 % Allowed : 19.38 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 758 helix: 1.17 (0.27), residues: 373 sheet: -0.88 (0.50), residues: 106 loop : -1.13 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.008 0.001 HIS C 111 PHE 0.028 0.001 PHE A 311 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6857 (p90) cc_final: 0.6227 (p90) REVERT: A 216 ASP cc_start: 0.7021 (t0) cc_final: 0.6594 (t0) REVERT: A 271 TRP cc_start: 0.5829 (p-90) cc_final: 0.5316 (p-90) REVERT: A 316 ASN cc_start: 0.7255 (t0) cc_final: 0.6515 (t0) REVERT: A 507 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6712 (tt) REVERT: A 606 GLU cc_start: 0.6304 (tt0) cc_final: 0.5998 (tt0) REVERT: A 615 GLU cc_start: 0.5412 (mp0) cc_final: 0.4886 (mp0) REVERT: C 31 MET cc_start: 0.1723 (mtm) cc_final: 0.1491 (mpp) REVERT: C 48 ASP cc_start: 0.7326 (t0) cc_final: 0.7077 (t0) REVERT: C 62 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6355 (mt0) REVERT: C 73 TYR cc_start: 0.7786 (m-80) cc_final: 0.7435 (m-80) REVERT: C 81 ARG cc_start: 0.7028 (tpm170) cc_final: 0.5142 (ptt90) REVERT: C 123 LYS cc_start: 0.7101 (mptt) cc_final: 0.6420 (tttm) REVERT: B 46 TYR cc_start: 0.6113 (m-80) cc_final: 0.5787 (m-80) REVERT: B 54 ASN cc_start: 0.7994 (m110) cc_final: 0.7757 (m-40) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.1625 time to fit residues: 20.2585 Evaluate side-chains 88 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.197062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175444 restraints weight = 8066.270| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.14 r_work: 0.3918 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.195 Angle : 0.534 7.827 8619 Z= 0.277 Chirality : 0.039 0.129 966 Planarity : 0.004 0.078 1048 Dihedral : 5.849 60.697 958 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.62 % Allowed : 19.38 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.32), residues: 758 helix: 1.02 (0.27), residues: 381 sheet: -0.75 (0.51), residues: 106 loop : -1.24 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.008 0.001 HIS C 111 PHE 0.029 0.001 PHE A 311 TYR 0.020 0.001 TYR A 176 ARG 0.004 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.7155 (p90) cc_final: 0.6460 (p90) REVERT: A 271 TRP cc_start: 0.6071 (p-90) cc_final: 0.5608 (p-90) REVERT: A 316 ASN cc_start: 0.7662 (t0) cc_final: 0.6940 (t0) REVERT: A 507 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7141 (tt) REVERT: A 606 GLU cc_start: 0.6235 (tt0) cc_final: 0.5935 (tt0) REVERT: A 615 GLU cc_start: 0.5556 (mp0) cc_final: 0.4926 (mp0) REVERT: C 31 MET cc_start: 0.1886 (mtm) cc_final: 0.1668 (mpp) REVERT: C 62 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6704 (mt0) REVERT: C 81 ARG cc_start: 0.7144 (tpm170) cc_final: 0.5323 (ptt90) REVERT: C 123 LYS cc_start: 0.7291 (mptt) cc_final: 0.6621 (tttm) REVERT: B 46 TYR cc_start: 0.6017 (m-80) cc_final: 0.5736 (m-80) REVERT: B 123 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6240 (t80) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.1647 time to fit residues: 18.9023 Evaluate side-chains 88 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.178317 restraints weight = 8047.232| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.14 r_work: 0.3920 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6326 Z= 0.164 Angle : 0.530 7.812 8619 Z= 0.274 Chirality : 0.039 0.127 966 Planarity : 0.004 0.077 1048 Dihedral : 5.734 57.442 958 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.31 % Allowed : 19.85 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.32), residues: 758 helix: 1.22 (0.27), residues: 373 sheet: -0.66 (0.51), residues: 106 loop : -1.10 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.006 0.001 HIS C 111 PHE 0.031 0.001 PHE A 311 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.7141 (p90) cc_final: 0.6395 (p90) REVERT: A 216 ASP cc_start: 0.7263 (t0) cc_final: 0.6794 (t0) REVERT: A 271 TRP cc_start: 0.6040 (p-90) cc_final: 0.5584 (p-90) REVERT: A 316 ASN cc_start: 0.7660 (t0) cc_final: 0.6961 (t0) REVERT: A 507 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7171 (tt) REVERT: A 606 GLU cc_start: 0.6205 (tt0) cc_final: 0.5908 (tt0) REVERT: A 615 GLU cc_start: 0.5552 (mp0) cc_final: 0.5003 (mp0) REVERT: C 62 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6745 (mt0) REVERT: C 81 ARG cc_start: 0.7170 (tpm170) cc_final: 0.5386 (ptt90) REVERT: C 123 LYS cc_start: 0.7232 (mptt) cc_final: 0.6576 (mmmt) REVERT: B 46 TYR cc_start: 0.5908 (m-80) cc_final: 0.5659 (m-80) REVERT: B 123 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6276 (t80) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.1591 time to fit residues: 19.0486 Evaluate side-chains 88 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174745 restraints weight = 8079.116| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.16 r_work: 0.3888 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.191 Angle : 0.540 7.901 8619 Z= 0.281 Chirality : 0.039 0.128 966 Planarity : 0.004 0.079 1048 Dihedral : 5.736 55.230 958 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 19.69 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.32), residues: 758 helix: 1.05 (0.27), residues: 382 sheet: -0.58 (0.51), residues: 106 loop : -1.28 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 151 HIS 0.008 0.001 HIS C 111 PHE 0.031 0.002 PHE A 311 TYR 0.020 0.001 TYR A 134 ARG 0.004 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.18 seconds wall clock time: 49 minutes 57.04 seconds (2997.04 seconds total)