Starting phenix.real_space_refine on Thu Mar 14 21:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/03_2024/5fn4_3239.pdb" } resolution = 4.0 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= 0.008 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 35 5.16 5 C 6398 2.51 5 N 1596 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9776 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 5.29, per 1000 atoms: 0.54 Number of scatterers: 9776 At special positions: 0 Unit cell: (91, 142.8, 103.6, 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 35 16.00 O 1747 8.00 N 1596 7.00 C 6398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.01 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.05 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 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: 3.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 60.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.354A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.862A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.640A pdb=" N ASN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.829A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.651A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.530A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.775A pdb=" N TYR A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.901A pdb=" N LEU A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 4.039A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.533A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 241 Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.503A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.420A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.626A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 100 removed outlier: 4.077A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.864A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.874A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 4.295A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 213 through 232 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.704A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 4.207A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.312A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 85 Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'G' and resid -1 through 23 Processing sheet with id= AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.673A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 59 through 60 Processing sheet with id= AC, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.425A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.635A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.172A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1737 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: 3.04 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1685 1.32 - 1.45: 2759 1.45 - 1.57: 5523 1.57 - 1.70: 8 1.70 - 1.82: 53 Bond restraints: 10028 Sorted by residual: bond pdb=" C LEU C 244 " pdb=" O LEU C 244 " ideal model delta sigma weight residual 1.231 1.380 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C HIS C 197 " pdb=" O HIS C 197 " ideal model delta sigma weight residual 1.236 1.304 -0.067 1.15e-02 7.56e+03 3.42e+01 bond pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.77e+01 bond pdb=" CA VAL B 255 " pdb=" CB VAL B 255 " ideal model delta sigma weight residual 1.540 1.582 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.17e-02 7.31e+03 1.28e+01 ... (remaining 10023 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.40: 308 106.40 - 113.48: 5136 113.48 - 120.57: 4031 120.57 - 127.65: 4093 127.65 - 134.74: 107 Bond angle restraints: 13675 Sorted by residual: angle pdb=" O ALA G 22 " pdb=" C ALA G 22 " pdb=" N ALA G 23 " ideal model delta sigma weight residual 122.07 109.70 12.37 1.03e+00 9.43e-01 1.44e+02 angle pdb=" O ALA G 21 " pdb=" C ALA G 21 " pdb=" N ALA G 22 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.44e+02 angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 111.62 118.93 -7.31 7.90e-01 1.60e+00 8.55e+01 angle pdb=" O VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.42 125.11 -4.69 6.40e-01 2.44e+00 5.38e+01 angle pdb=" CA LEU C 169 " pdb=" C LEU C 169 " pdb=" N LEU C 170 " ideal model delta sigma weight residual 117.07 108.87 8.20 1.14e+00 7.69e-01 5.18e+01 ... (remaining 13670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4964 17.74 - 35.47: 643 35.47 - 53.21: 188 53.21 - 70.95: 44 70.95 - 88.68: 12 Dihedral angle restraints: 5851 sinusoidal: 2208 harmonic: 3643 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual 93.00 168.51 -75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1310 0.120 - 0.240: 235 0.240 - 0.360: 30 0.360 - 0.480: 8 0.480 - 0.600: 1 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CA PHE A 218 " pdb=" N PHE A 218 " pdb=" C PHE A 218 " pdb=" CB PHE A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA LEU A 312 " pdb=" N LEU A 312 " pdb=" C LEU A 312 " pdb=" CB LEU A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 1581 not shown) Planarity restraints: 1706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 21 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ALA G 21 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 21 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 22 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 22 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.55e+02 pdb=" C ALA G 22 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 22 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 23 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 175 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C PHE B 175 " -0.073 2.00e-02 2.50e+03 pdb=" O PHE B 175 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE B 176 " 0.025 2.00e-02 2.50e+03 ... (remaining 1703 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 180 2.69 - 3.24: 10256 3.24 - 3.79: 16234 3.79 - 4.35: 20802 4.35 - 4.90: 32959 Nonbonded interactions: 80431 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG SER C 124 " model vdw 2.131 2.440 nonbonded pdb=" O HIS C 197 " pdb=" OG1 THR C 200 " model vdw 2.252 2.440 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.267 2.440 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.277 2.440 nonbonded pdb=" O ARG A 232 " pdb=" OG SER A 235 " model vdw 2.294 2.440 ... (remaining 80426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.840 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.740 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 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 : 0.010 0.149 10028 Z= 0.644 Angle : 1.713 12.399 13675 Z= 1.236 Chirality : 0.096 0.600 1584 Planarity : 0.009 0.125 1706 Dihedral : 18.066 88.682 3484 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 3.24 % Allowed : 11.98 % Favored : 84.78 % Rotamer: Outliers : 10.51 % Allowed : 14.90 % Favored : 74.59 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 3.64 % 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: -1.44 (0.21), residues: 1235 helix: 1.03 (0.16), residues: 712 sheet: -3.69 (0.40), residues: 110 loop : -3.87 (0.25), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 36 HIS 0.017 0.003 HIS A 553 PHE 0.044 0.004 PHE B 176 TYR 0.043 0.004 TYR C 69 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 316 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.9434 (mt) cc_final: 0.9226 (mt) REVERT: A 95 MET cc_start: 0.8348 (mmt) cc_final: 0.7925 (mmm) REVERT: A 100 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 215 MET cc_start: 0.8953 (ttp) cc_final: 0.8743 (ptm) REVERT: A 217 LEU cc_start: 0.8876 (tt) cc_final: 0.8541 (pt) REVERT: A 231 MET cc_start: 0.8855 (mmp) cc_final: 0.8583 (mmm) REVERT: A 249 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 259 MET cc_start: 0.9163 (tpp) cc_final: 0.8757 (mmm) REVERT: A 331 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7703 (tp40) REVERT: A 347 MET cc_start: 0.9318 (mtm) cc_final: 0.9057 (mpp) REVERT: A 362 PHE cc_start: 0.8225 (t80) cc_final: 0.7950 (t80) REVERT: A 474 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (pp20) REVERT: A 543 ARG cc_start: 0.8527 (ptm-80) cc_final: 0.7886 (tpt170) REVERT: A 548 ASP cc_start: 0.9101 (t0) cc_final: 0.8835 (m-30) REVERT: A 574 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 575 THR cc_start: 0.7571 (p) cc_final: 0.7207 (p) REVERT: A 649 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.6472 (t) REVERT: B 93 MET cc_start: 0.9294 (mtm) cc_final: 0.9071 (mmt) REVERT: B 106 TYR cc_start: 0.8629 (m-80) cc_final: 0.8246 (m-80) REVERT: B 167 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6393 (tp) REVERT: B 184 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8585 (mm-30) REVERT: B 223 GLN cc_start: 0.8384 (mt0) cc_final: 0.7849 (mm-40) REVERT: B 244 TRP cc_start: 0.5553 (OUTLIER) cc_final: 0.4638 (m100) REVERT: B 389 TYR cc_start: 0.8875 (m-80) cc_final: 0.8174 (m-80) REVERT: B 399 THR cc_start: 0.7568 (m) cc_final: 0.7333 (t) REVERT: B 419 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9010 (m) REVERT: B 456 PHE cc_start: 0.9405 (t80) cc_final: 0.9175 (t80) REVERT: C 24 THR cc_start: 0.9022 (m) cc_final: 0.8773 (p) REVERT: C 53 TRP cc_start: 0.8627 (t60) cc_final: 0.7886 (t60) REVERT: C 91 TYR cc_start: 0.8963 (t80) cc_final: 0.8735 (t80) REVERT: C 99 GLU cc_start: 0.8916 (pt0) cc_final: 0.8684 (pt0) REVERT: D 84 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8485 (mpt-90) REVERT: D 95 THR cc_start: 0.8328 (m) cc_final: 0.8011 (p) outliers start: 110 outliers final: 34 residues processed: 384 average time/residue: 0.2080 time to fit residues: 111.6413 Evaluate side-chains 262 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 85 TRP Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 305 GLN A 331 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN A 612 ASN B 223 GLN D 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10028 Z= 0.248 Angle : 0.820 10.731 13675 Z= 0.415 Chirality : 0.046 0.198 1584 Planarity : 0.006 0.062 1706 Dihedral : 10.041 66.408 1420 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 1.38 % Allowed : 7.94 % Favored : 90.69 % Rotamer: Outliers : 6.69 % Allowed : 20.63 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.35 (0.25), residues: 1235 helix: 2.62 (0.19), residues: 719 sheet: -3.22 (0.37), residues: 119 loop : -3.43 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 36 HIS 0.012 0.002 HIS A 553 PHE 0.031 0.002 PHE A 302 TYR 0.022 0.002 TYR A 565 ARG 0.007 0.001 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 252 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8945 (p0) cc_final: 0.8709 (t0) REVERT: A 91 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8153 (p0) REVERT: A 95 MET cc_start: 0.8363 (mmt) cc_final: 0.8075 (mmm) REVERT: A 217 LEU cc_start: 0.8474 (tt) cc_final: 0.8234 (pt) REVERT: A 221 MET cc_start: 0.8442 (mmm) cc_final: 0.7827 (mmp) REVERT: A 249 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: A 253 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7742 (p0) REVERT: A 257 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.7046 (p-90) REVERT: A 362 PHE cc_start: 0.8299 (t80) cc_final: 0.7525 (t80) REVERT: A 378 MET cc_start: 0.8202 (mpt) cc_final: 0.7778 (mpp) REVERT: B 103 VAL cc_start: 0.5584 (t) cc_final: 0.5291 (t) REVERT: B 168 ILE cc_start: 0.7296 (mm) cc_final: 0.6850 (mm) REVERT: B 184 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: B 223 GLN cc_start: 0.8076 (mt0) cc_final: 0.7774 (mm-40) REVERT: B 399 THR cc_start: 0.7248 (m) cc_final: 0.7033 (t) REVERT: C 83 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8791 (mm-40) REVERT: C 117 MET cc_start: 0.8764 (mtp) cc_final: 0.8455 (ppp) REVERT: D 6 VAL cc_start: 0.8640 (t) cc_final: 0.8439 (p) REVERT: D 78 PHE cc_start: 0.8173 (t80) cc_final: 0.7941 (t80) outliers start: 70 outliers final: 35 residues processed: 299 average time/residue: 0.1764 time to fit residues: 77.5803 Evaluate side-chains 240 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN B 190 ASN B 464 GLN C 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10028 Z= 0.317 Angle : 0.812 19.002 13675 Z= 0.404 Chirality : 0.046 0.299 1584 Planarity : 0.006 0.064 1706 Dihedral : 8.254 60.017 1378 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.26 % Favored : 90.77 % Rotamer: Outliers : 7.93 % Allowed : 22.25 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.12 (0.25), residues: 1235 helix: 1.97 (0.19), residues: 726 sheet: -2.80 (0.40), residues: 111 loop : -3.34 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 174 HIS 0.006 0.001 HIS A 553 PHE 0.038 0.002 PHE B 465 TYR 0.025 0.002 TYR B 225 ARG 0.004 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 201 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8031 (p0) REVERT: A 95 MET cc_start: 0.8371 (mmt) cc_final: 0.7967 (mmm) REVERT: A 108 MET cc_start: 0.9201 (tpp) cc_final: 0.8994 (tpp) REVERT: A 173 TYR cc_start: 0.2435 (t80) cc_final: 0.2205 (t80) REVERT: A 215 MET cc_start: 0.8610 (ttp) cc_final: 0.8353 (ptm) REVERT: A 217 LEU cc_start: 0.8414 (tt) cc_final: 0.8130 (tp) REVERT: A 221 MET cc_start: 0.8607 (mmm) cc_final: 0.8384 (mmp) REVERT: A 259 MET cc_start: 0.8898 (mmm) cc_final: 0.8661 (mmm) REVERT: A 362 PHE cc_start: 0.8874 (t80) cc_final: 0.7978 (t80) REVERT: A 439 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7739 (p) REVERT: B 93 MET cc_start: 0.9214 (mtm) cc_final: 0.8994 (mmt) REVERT: B 223 GLN cc_start: 0.8006 (mt0) cc_final: 0.7633 (mm-40) REVERT: B 399 THR cc_start: 0.7275 (m) cc_final: 0.7067 (t) REVERT: B 458 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: C 83 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8703 (mm-40) outliers start: 83 outliers final: 45 residues processed: 250 average time/residue: 0.1595 time to fit residues: 60.2586 Evaluate side-chains 223 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 TRP Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 116 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10028 Z= 0.301 Angle : 0.776 11.350 13675 Z= 0.386 Chirality : 0.045 0.307 1584 Planarity : 0.005 0.065 1706 Dihedral : 7.301 57.811 1363 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.61 % Favored : 91.58 % Rotamer: Outliers : 5.92 % Allowed : 24.74 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.20 (0.25), residues: 1235 helix: 1.88 (0.19), residues: 713 sheet: -2.64 (0.41), residues: 117 loop : -3.22 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 174 HIS 0.006 0.001 HIS A 553 PHE 0.038 0.002 PHE B 465 TYR 0.022 0.002 TYR A 554 ARG 0.005 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 188 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.9038 (p0) cc_final: 0.8678 (t0) REVERT: A 91 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8232 (p0) REVERT: A 95 MET cc_start: 0.8400 (mmt) cc_final: 0.7843 (mmt) REVERT: A 173 TYR cc_start: 0.2271 (t80) cc_final: 0.1748 (t80) REVERT: A 215 MET cc_start: 0.8425 (ttp) cc_final: 0.8136 (ptm) REVERT: A 217 LEU cc_start: 0.8449 (tt) cc_final: 0.8137 (pt) REVERT: A 221 MET cc_start: 0.8547 (mmm) cc_final: 0.7849 (mmp) REVERT: A 362 PHE cc_start: 0.8914 (t80) cc_final: 0.8268 (t80) REVERT: B 223 GLN cc_start: 0.8062 (mt0) cc_final: 0.7714 (mm-40) REVERT: B 441 PHE cc_start: 0.8732 (m-80) cc_final: 0.8497 (m-80) REVERT: B 459 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8494 (tp-100) REVERT: C 83 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: C 140 ASP cc_start: 0.7775 (m-30) cc_final: 0.7415 (m-30) outliers start: 62 outliers final: 47 residues processed: 232 average time/residue: 0.1577 time to fit residues: 55.5780 Evaluate side-chains 218 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 367 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 116 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10028 Z= 0.346 Angle : 0.775 12.234 13675 Z= 0.387 Chirality : 0.044 0.306 1584 Planarity : 0.005 0.065 1706 Dihedral : 7.216 58.820 1363 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.26 % Favored : 90.93 % Rotamer: Outliers : 7.45 % Allowed : 25.02 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.30 (0.24), residues: 1235 helix: 1.63 (0.19), residues: 723 sheet: -2.30 (0.42), residues: 111 loop : -3.15 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 67 HIS 0.008 0.002 HIS A 102 PHE 0.033 0.002 PHE B 465 TYR 0.023 0.002 TYR B 225 ARG 0.003 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 176 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.9009 (p0) cc_final: 0.8729 (t0) REVERT: A 91 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8285 (p0) REVERT: A 95 MET cc_start: 0.8485 (mmt) cc_final: 0.7906 (mmt) REVERT: A 173 TYR cc_start: 0.2351 (t80) cc_final: 0.1910 (t80) REVERT: A 195 CYS cc_start: 0.8118 (m) cc_final: 0.7814 (m) REVERT: A 217 LEU cc_start: 0.8344 (tt) cc_final: 0.7979 (pt) REVERT: A 221 MET cc_start: 0.8463 (mmm) cc_final: 0.7675 (mmp) REVERT: A 305 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8659 (tt0) REVERT: A 347 MET cc_start: 0.8820 (mtm) cc_final: 0.8616 (mtm) REVERT: A 362 PHE cc_start: 0.8921 (t80) cc_final: 0.8435 (t80) REVERT: C 83 GLN cc_start: 0.9070 (mt0) cc_final: 0.8701 (mm-40) outliers start: 78 outliers final: 56 residues processed: 234 average time/residue: 0.1620 time to fit residues: 57.9463 Evaluate side-chains 225 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 TRP Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 114 optimal weight: 10.0000 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 464 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10028 Z= 0.227 Angle : 0.750 13.822 13675 Z= 0.365 Chirality : 0.044 0.296 1584 Planarity : 0.005 0.064 1706 Dihedral : 6.966 59.682 1363 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.29 % Favored : 91.90 % Rotamer: Outliers : 5.25 % Allowed : 28.27 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.12 (0.24), residues: 1235 helix: 1.72 (0.19), residues: 714 sheet: -2.03 (0.42), residues: 111 loop : -2.92 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.027 0.002 PHE A 302 TYR 0.023 0.002 TYR B 389 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.9101 (p0) cc_final: 0.8849 (t0) REVERT: A 95 MET cc_start: 0.8504 (mmt) cc_final: 0.8137 (mmt) REVERT: A 217 LEU cc_start: 0.8353 (tt) cc_final: 0.7979 (pt) REVERT: A 221 MET cc_start: 0.8396 (mmm) cc_final: 0.7996 (mmp) REVERT: A 305 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8619 (tt0) REVERT: A 362 PHE cc_start: 0.8911 (t80) cc_final: 0.8490 (t80) REVERT: B 92 CYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 93 MET cc_start: 0.9228 (mtm) cc_final: 0.8992 (mmt) REVERT: B 210 MET cc_start: 0.9486 (tpt) cc_final: 0.9285 (mmm) REVERT: B 441 PHE cc_start: 0.8297 (m-80) cc_final: 0.8093 (m-80) REVERT: C 83 GLN cc_start: 0.9099 (mt0) cc_final: 0.8751 (mm-40) outliers start: 55 outliers final: 42 residues processed: 222 average time/residue: 0.1600 time to fit residues: 53.9990 Evaluate side-chains 206 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10028 Z= 0.219 Angle : 0.762 13.750 13675 Z= 0.369 Chirality : 0.043 0.281 1584 Planarity : 0.005 0.068 1706 Dihedral : 6.556 57.490 1360 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.96 % Favored : 92.23 % Rotamer: Outliers : 4.49 % Allowed : 30.28 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.24), residues: 1235 helix: 1.64 (0.19), residues: 717 sheet: -1.87 (0.43), residues: 111 loop : -2.85 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.017 0.001 TYR B 225 ARG 0.007 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.9126 (p0) cc_final: 0.8901 (t0) REVERT: A 95 MET cc_start: 0.8402 (mmt) cc_final: 0.7720 (mmt) REVERT: A 237 GLN cc_start: 0.9059 (mt0) cc_final: 0.8846 (pt0) REVERT: A 305 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8589 (tt0) REVERT: A 362 PHE cc_start: 0.8898 (t80) cc_final: 0.8448 (t80) REVERT: B 210 MET cc_start: 0.9485 (tpt) cc_final: 0.9058 (mmt) REVERT: B 441 PHE cc_start: 0.8321 (m-80) cc_final: 0.8070 (m-80) REVERT: C 83 GLN cc_start: 0.9120 (mt0) cc_final: 0.8773 (mm-40) REVERT: C 119 TYR cc_start: 0.7886 (t80) cc_final: 0.7651 (t80) REVERT: D 59 ARG cc_start: 0.6630 (ttm-80) cc_final: 0.6412 (ttm110) outliers start: 47 outliers final: 39 residues processed: 214 average time/residue: 0.1839 time to fit residues: 58.8925 Evaluate side-chains 202 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10028 Z= 0.259 Angle : 0.767 13.015 13675 Z= 0.376 Chirality : 0.044 0.293 1584 Planarity : 0.005 0.067 1706 Dihedral : 6.045 57.510 1356 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.45 % Favored : 91.82 % Rotamer: Outliers : 4.97 % Allowed : 30.37 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.15 (0.25), residues: 1235 helix: 1.63 (0.19), residues: 710 sheet: -1.98 (0.42), residues: 116 loop : -2.77 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 174 HIS 0.004 0.001 HIS A 553 PHE 0.026 0.002 PHE A 302 TYR 0.023 0.001 TYR B 466 ARG 0.011 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8130 (mmt) cc_final: 0.7450 (mmt) REVERT: A 305 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8598 (tt0) REVERT: A 362 PHE cc_start: 0.8897 (t80) cc_final: 0.8436 (t80) REVERT: B 92 CYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8378 (p) REVERT: B 93 MET cc_start: 0.9221 (mtm) cc_final: 0.8990 (mmt) REVERT: B 441 PHE cc_start: 0.8354 (m-80) cc_final: 0.8084 (m-80) REVERT: C 83 GLN cc_start: 0.9097 (mt0) cc_final: 0.8732 (mm-40) REVERT: C 119 TYR cc_start: 0.7886 (t80) cc_final: 0.7667 (t80) outliers start: 52 outliers final: 41 residues processed: 206 average time/residue: 0.1731 time to fit residues: 53.7389 Evaluate side-chains 201 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10028 Z= 0.219 Angle : 0.797 14.443 13675 Z= 0.384 Chirality : 0.045 0.315 1584 Planarity : 0.005 0.068 1706 Dihedral : 5.845 57.272 1354 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.80 % Favored : 92.39 % Rotamer: Outliers : 4.30 % Allowed : 30.85 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.25), residues: 1235 helix: 1.61 (0.19), residues: 708 sheet: -2.02 (0.42), residues: 119 loop : -2.65 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 174 HIS 0.004 0.001 HIS C 197 PHE 0.029 0.002 PHE A 302 TYR 0.017 0.001 TYR B 106 ARG 0.009 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.9068 (p0) cc_final: 0.8840 (t0) REVERT: A 305 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8610 (tt0) REVERT: B 92 CYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8273 (p) REVERT: B 93 MET cc_start: 0.9218 (mtm) cc_final: 0.8992 (mmt) REVERT: B 195 TYR cc_start: 0.7738 (m-80) cc_final: 0.7503 (m-80) REVERT: B 210 MET cc_start: 0.9478 (tpt) cc_final: 0.9244 (mmm) REVERT: B 441 PHE cc_start: 0.8443 (m-80) cc_final: 0.8132 (m-80) REVERT: C 83 GLN cc_start: 0.9112 (mt0) cc_final: 0.8758 (mm-40) outliers start: 45 outliers final: 38 residues processed: 205 average time/residue: 0.1637 time to fit residues: 51.0703 Evaluate side-chains 202 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.0030 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN B 190 ASN B 223 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10028 Z= 0.364 Angle : 0.840 14.380 13675 Z= 0.423 Chirality : 0.047 0.305 1584 Planarity : 0.005 0.069 1706 Dihedral : 6.048 55.947 1354 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.34 % Favored : 90.85 % Rotamer: Outliers : 4.11 % Allowed : 31.61 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.34 (0.25), residues: 1235 helix: 1.41 (0.19), residues: 714 sheet: -2.10 (0.41), residues: 119 loop : -2.73 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP C 174 HIS 0.007 0.002 HIS A 102 PHE 0.029 0.002 PHE B 105 TYR 0.017 0.002 TYR B 195 ARG 0.010 0.001 ARG D 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 CYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 93 MET cc_start: 0.9230 (mtm) cc_final: 0.9011 (mmt) REVERT: B 195 TYR cc_start: 0.7651 (m-80) cc_final: 0.7398 (m-80) REVERT: B 223 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7454 (mm-40) REVERT: C 83 GLN cc_start: 0.9060 (mt0) cc_final: 0.8658 (mm-40) outliers start: 43 outliers final: 39 residues processed: 202 average time/residue: 0.1633 time to fit residues: 50.0250 Evaluate side-chains 202 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057755 restraints weight = 48285.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059403 restraints weight = 27576.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060485 restraints weight = 18106.716| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10028 Z= 0.224 Angle : 0.849 14.273 13675 Z= 0.413 Chirality : 0.046 0.296 1584 Planarity : 0.005 0.069 1706 Dihedral : 5.886 57.469 1354 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.72 % Favored : 92.47 % Rotamer: Outliers : 3.82 % Allowed : 32.19 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.28 (0.25), residues: 1235 helix: 1.46 (0.19), residues: 707 sheet: -2.10 (0.41), residues: 127 loop : -2.62 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 174 HIS 0.003 0.001 HIS C 58 PHE 0.041 0.002 PHE C 132 TYR 0.016 0.001 TYR A 565 ARG 0.009 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.23 seconds wall clock time: 37 minutes 35.96 seconds (2255.96 seconds total)