Starting phenix.real_space_refine on Wed Sep 25 07:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/09_2024/5fn4_3239.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/09_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_3239/09_2024/5fn4_3239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/09_2024/5fn4_3239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/09_2024/5fn4_3239.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/09_2024/5fn4_3239.cif" } 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. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.42, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 2.85 Time building geometry restraints manager: 3.10 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: 0.00 - 2.48: 11458 2.48 - 4.96: 2064 4.96 - 7.44: 121 7.44 - 9.92: 26 9.92 - 12.40: 6 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 3.040 nonbonded pdb=" O HIS C 197 " pdb=" OG1 THR C 200 " model vdw 2.252 3.040 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.267 3.040 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.277 3.040 nonbonded pdb=" O ARG A 232 " pdb=" OG SER A 235 " model vdw 2.294 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- 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 : 1.151 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: 0.2104 time to fit residues: 112.7908 Evaluate side-chains 262 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 355 GLN A 417 ASN A 428 GLN A 450 ASN A 478 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN B 223 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10028 Z= 0.235 Angle : 0.839 10.853 13675 Z= 0.422 Chirality : 0.046 0.209 1584 Planarity : 0.006 0.061 1706 Dihedral : 9.999 66.372 1420 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 1.38 % Allowed : 7.77 % Favored : 90.85 % Rotamer: Outliers : 6.30 % Allowed : 20.15 % Favored : 73.54 % 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: 2.60 (0.19), residues: 716 sheet: -3.18 (0.37), residues: 119 loop : -3.39 (0.27), residues: 400 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 0.021 0.002 TYR A 565 ARG 0.004 0.001 ARG C 237 *********************** 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 329 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 1.038 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: A 34 ASN cc_start: 0.8902 (p0) cc_final: 0.8687 (t0) REVERT: A 91 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 95 MET cc_start: 0.8361 (mmt) cc_final: 0.8122 (mmm) REVERT: A 217 LEU cc_start: 0.8629 (tt) cc_final: 0.8383 (pp) REVERT: A 221 MET cc_start: 0.8434 (mmm) cc_final: 0.7931 (mmp) REVERT: A 249 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: A 257 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.7046 (p-90) REVERT: A 362 PHE cc_start: 0.8297 (t80) cc_final: 0.7437 (t80) REVERT: A 378 MET cc_start: 0.8213 (mpt) cc_final: 0.7799 (mpp) REVERT: A 428 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: B 168 ILE cc_start: 0.7432 (mm) cc_final: 0.6998 (mm) REVERT: B 184 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (mm-30) REVERT: B 223 GLN cc_start: 0.8076 (mt0) cc_final: 0.7774 (mm-40) REVERT: C 83 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8856 (mm-40) REVERT: C 117 MET cc_start: 0.8765 (mtp) cc_final: 0.8475 (ppp) REVERT: D 6 VAL cc_start: 0.8634 (t) cc_final: 0.8418 (p) outliers start: 66 outliers final: 30 residues processed: 307 average time/residue: 0.1832 time to fit residues: 82.7021 Evaluate side-chains 224 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 428 GLN 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 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 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 46 LEU 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 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 A 313 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 606 GLN B 190 ASN B 454 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 10028 Z= 0.392 Angle : 0.858 21.016 13675 Z= 0.431 Chirality : 0.047 0.310 1584 Planarity : 0.006 0.067 1706 Dihedral : 8.098 58.527 1375 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.42 % Favored : 90.69 % Rotamer: Outliers : 8.02 % Allowed : 20.63 % Favored : 71.35 % 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: -0.22 (0.25), residues: 1235 helix: 1.90 (0.19), residues: 717 sheet: -2.87 (0.39), residues: 118 loop : -3.28 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 174 HIS 0.008 0.002 HIS A 553 PHE 0.043 0.002 PHE B 465 TYR 0.026 0.002 TYR B 225 ARG 0.003 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 278 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 194 time to evaluate : 1.156 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: A 91 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 95 MET cc_start: 0.8407 (mmt) cc_final: 0.7827 (mmt) REVERT: A 108 MET cc_start: 0.9217 (tpp) cc_final: 0.9013 (tpp) REVERT: A 173 TYR cc_start: 0.1482 (t80) cc_final: 0.1228 (t80) REVERT: A 215 MET cc_start: 0.8767 (ttp) cc_final: 0.8366 (ptm) REVERT: A 217 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8143 (pt) REVERT: A 221 MET cc_start: 0.8594 (mmm) cc_final: 0.8055 (mmp) REVERT: A 253 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 362 PHE cc_start: 0.8850 (t80) cc_final: 0.7829 (t80) REVERT: A 439 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7676 (p) REVERT: B 93 MET cc_start: 0.9242 (mtm) cc_final: 0.9009 (mmp) REVERT: B 223 GLN cc_start: 0.8047 (mt0) cc_final: 0.7671 (mm-40) REVERT: B 456 PHE cc_start: 0.9304 (t80) cc_final: 0.9079 (t80) REVERT: C 83 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8692 (mm-40) REVERT: D 64 PHE cc_start: 0.8564 (t80) cc_final: 0.8195 (t80) outliers start: 84 outliers final: 51 residues processed: 246 average time/residue: 0.1700 time to fit residues: 62.6325 Evaluate side-chains 233 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP 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 325 VAL 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 537 ILE Chi-restraints excluded: chain A residue 587 GLN 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 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 VAL 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 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP 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 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 68 VAL 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: 0.5980 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN B 190 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10028 Z= 0.235 Angle : 0.795 11.908 13675 Z= 0.386 Chirality : 0.046 0.316 1584 Planarity : 0.005 0.061 1706 Dihedral : 7.311 59.671 1362 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.37 % Favored : 91.82 % Rotamer: Outliers : 5.92 % Allowed : 23.69 % Favored : 70.39 % 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 (0.24), residues: 1235 helix: 1.78 (0.19), residues: 722 sheet: -2.45 (0.43), residues: 118 loop : -3.17 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 174 HIS 0.005 0.001 HIS A 553 PHE 0.036 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 258 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 196 time to evaluate : 1.612 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: A 34 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (t0) REVERT: A 95 MET cc_start: 0.8409 (mmt) cc_final: 0.7954 (mmt) REVERT: A 173 TYR cc_start: 0.1718 (t80) cc_final: 0.1256 (t80) REVERT: A 217 LEU cc_start: 0.8382 (tt) cc_final: 0.8037 (pt) REVERT: A 221 MET cc_start: 0.8542 (mmm) cc_final: 0.7863 (mmp) REVERT: A 253 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 259 MET cc_start: 0.8420 (mmm) cc_final: 0.7835 (tpt) REVERT: A 305 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8878 (tt0) REVERT: A 362 PHE cc_start: 0.8900 (t80) cc_final: 0.8298 (t80) REVERT: A 439 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7864 (p) REVERT: A 591 LYS cc_start: 0.9550 (ttpp) cc_final: 0.9327 (pttp) REVERT: B 93 MET cc_start: 0.9247 (mtm) cc_final: 0.8984 (mmt) REVERT: B 223 GLN cc_start: 0.8018 (mt0) cc_final: 0.7654 (mm-40) REVERT: B 441 PHE cc_start: 0.8726 (m-80) cc_final: 0.8494 (m-80) REVERT: B 456 PHE cc_start: 0.9366 (t80) cc_final: 0.9164 (t80) REVERT: C 83 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8723 (mm-40) REVERT: D 64 PHE cc_start: 0.8641 (t80) cc_final: 0.8280 (t80) outliers start: 62 outliers final: 37 residues processed: 233 average time/residue: 0.1832 time to fit residues: 65.3980 Evaluate side-chains 214 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER 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 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU 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 537 ILE Chi-restraints excluded: chain A residue 587 GLN 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 660 ILE Chi-restraints excluded: chain B residue 94 VAL 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 412 VAL Chi-restraints excluded: chain B residue 458 ASP 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 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU 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: 4.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10028 Z= 0.344 Angle : 0.788 12.454 13675 Z= 0.396 Chirality : 0.045 0.300 1584 Planarity : 0.005 0.061 1706 Dihedral : 7.120 59.219 1360 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.94 % Favored : 91.26 % Rotamer: Outliers : 7.26 % Allowed : 23.78 % Favored : 68.96 % 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: 1.65 (0.19), residues: 714 sheet: -2.35 (0.44), residues: 110 loop : -3.06 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 174 HIS 0.009 0.002 HIS C 58 PHE 0.038 0.002 PHE B 465 TYR 0.027 0.002 TYR B 181 ARG 0.003 0.000 ARG A 371 *********************** 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 258 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 182 time to evaluate : 1.068 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: 0.8453 (OUTLIER) cc_final: 0.8086 (p0) REVERT: A 95 MET cc_start: 0.8384 (mmt) cc_final: 0.7574 (mmt) REVERT: A 173 TYR cc_start: 0.2213 (t80) cc_final: 0.1812 (t80) REVERT: A 217 LEU cc_start: 0.8235 (tt) cc_final: 0.8031 (pt) REVERT: A 221 MET cc_start: 0.8528 (mmm) cc_final: 0.7740 (mmp) REVERT: A 253 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7740 (p0) REVERT: A 259 MET cc_start: 0.8391 (mmm) cc_final: 0.7956 (tpt) REVERT: A 305 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8722 (tt0) REVERT: A 362 PHE cc_start: 0.8948 (t80) cc_final: 0.8423 (t80) REVERT: A 439 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 93 MET cc_start: 0.9255 (mtm) cc_final: 0.8993 (mmt) REVERT: C 83 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8726 (mm-40) outliers start: 76 outliers final: 49 residues processed: 234 average time/residue: 0.1884 time to fit residues: 66.5169 Evaluate side-chains 224 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 100 SER 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 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 537 ILE Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN 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 640 TRP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 180 ILE 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 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 452 LEU Chi-restraints excluded: chain B residue 458 ASP 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 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU 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: 0.9980 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5938 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10028 Z= 0.226 Angle : 0.790 13.814 13675 Z= 0.378 Chirality : 0.044 0.290 1584 Planarity : 0.005 0.060 1706 Dihedral : 6.697 58.206 1360 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.72 % Favored : 92.55 % Rotamer: Outliers : 4.97 % Allowed : 26.55 % Favored : 68.48 % 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: -0.23 (0.24), residues: 1235 helix: 1.58 (0.19), residues: 719 sheet: -2.02 (0.46), residues: 104 loop : -2.92 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.035 0.002 PHE B 465 TYR 0.022 0.001 TYR B 389 ARG 0.004 0.000 ARG D 5 *********************** 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 248 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 95 MET cc_start: 0.8582 (mmt) cc_final: 0.8065 (mmt) REVERT: A 173 TYR cc_start: 0.1960 (t80) cc_final: 0.1530 (t80) REVERT: A 217 LEU cc_start: 0.8261 (tt) cc_final: 0.8053 (pt) REVERT: A 221 MET cc_start: 0.8415 (mmm) cc_final: 0.8059 (mmp) REVERT: A 237 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8752 (mt0) REVERT: A 253 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7606 (p0) REVERT: A 259 MET cc_start: 0.8211 (mmm) cc_final: 0.7713 (tpt) REVERT: A 305 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8876 (tt0) REVERT: A 362 PHE cc_start: 0.8940 (t80) cc_final: 0.8540 (t80) REVERT: A 591 LYS cc_start: 0.9519 (ttpp) cc_final: 0.9261 (pttp) REVERT: B 93 MET cc_start: 0.9242 (mtm) cc_final: 0.8965 (mmt) REVERT: B 441 PHE cc_start: 0.8303 (m-80) cc_final: 0.8102 (m-80) REVERT: B 457 MET cc_start: 0.8978 (mmt) cc_final: 0.8499 (mmt) REVERT: C 83 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8827 (mm-40) outliers start: 52 outliers final: 32 residues processed: 230 average time/residue: 0.1683 time to fit residues: 58.7048 Evaluate side-chains 215 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 100 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 237 GLN 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 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 565 TYR 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 229 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 458 ASP 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 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 237 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 223 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5955 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10028 Z= 0.224 Angle : 0.797 13.862 13675 Z= 0.383 Chirality : 0.046 0.372 1584 Planarity : 0.005 0.071 1706 Dihedral : 6.092 59.789 1354 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.45 % Favored : 91.90 % Rotamer: Outliers : 4.39 % Allowed : 27.51 % Favored : 68.10 % 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 (0.24), residues: 1235 helix: 1.52 (0.19), residues: 715 sheet: -2.06 (0.44), residues: 111 loop : -2.85 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.043 0.002 PHE B 456 TYR 0.020 0.001 TYR B 389 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 234 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8376 (mmt) cc_final: 0.7746 (mmt) REVERT: A 173 TYR cc_start: 0.1716 (t80) cc_final: 0.1288 (t80) REVERT: A 221 MET cc_start: 0.8448 (mmm) cc_final: 0.7617 (mmp) REVERT: A 253 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 259 MET cc_start: 0.8238 (mmm) cc_final: 0.7766 (tpt) REVERT: A 305 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8873 (tt0) REVERT: A 347 MET cc_start: 0.8727 (mpp) cc_final: 0.8483 (mpp) REVERT: A 362 PHE cc_start: 0.9006 (t80) cc_final: 0.8651 (t80) REVERT: A 591 LYS cc_start: 0.9521 (ttpp) cc_final: 0.9255 (pttp) REVERT: B 93 MET cc_start: 0.9222 (mtm) cc_final: 0.8974 (mmt) REVERT: B 210 MET cc_start: 0.9124 (mmm) cc_final: 0.8588 (mmt) REVERT: B 223 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: B 441 PHE cc_start: 0.8329 (m-80) cc_final: 0.8030 (m-80) REVERT: B 457 MET cc_start: 0.8932 (mmt) cc_final: 0.8725 (mmt) REVERT: C 218 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7851 (m-10) outliers start: 46 outliers final: 37 residues processed: 213 average time/residue: 0.1725 time to fit residues: 56.2792 Evaluate side-chains 211 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 SER 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 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE 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 565 TYR 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 660 ILE Chi-restraints excluded: chain B residue 80 LYS 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 403 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP 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 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 overall best weight: 2.5142 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 223 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5976 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10028 Z= 0.278 Angle : 0.796 13.518 13675 Z= 0.388 Chirality : 0.045 0.299 1584 Planarity : 0.005 0.061 1706 Dihedral : 6.036 56.636 1354 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.77 % Favored : 91.58 % Rotamer: Outliers : 4.78 % Allowed : 27.79 % Favored : 67.43 % 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: -0.37 (0.24), residues: 1235 helix: 1.40 (0.19), residues: 715 sheet: -2.21 (0.42), residues: 116 loop : -2.76 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 174 HIS 0.005 0.001 HIS A 553 PHE 0.049 0.002 PHE B 456 TYR 0.017 0.001 TYR A 569 ARG 0.005 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 234 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 1.175 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: A 95 MET cc_start: 0.8076 (mmt) cc_final: 0.7436 (mmt) REVERT: A 253 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7796 (p0) REVERT: A 259 MET cc_start: 0.8328 (mmm) cc_final: 0.7851 (tpt) REVERT: A 305 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8887 (tt0) REVERT: A 362 PHE cc_start: 0.8977 (t80) cc_final: 0.8637 (t80) REVERT: A 591 LYS cc_start: 0.9517 (ttpp) cc_final: 0.9250 (pttp) REVERT: B 93 MET cc_start: 0.9222 (mtm) cc_final: 0.8972 (mmt) REVERT: B 210 MET cc_start: 0.9229 (mmm) cc_final: 0.8734 (mmt) REVERT: B 223 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7511 (mm-40) REVERT: B 441 PHE cc_start: 0.8302 (m-80) cc_final: 0.8052 (m-80) REVERT: C 218 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (m-10) outliers start: 50 outliers final: 41 residues processed: 216 average time/residue: 0.1733 time to fit residues: 56.1083 Evaluate side-chains 211 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER 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 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE 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 565 TYR 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 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL 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 403 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR 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: 8.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** B 190 ASN ** B 454 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: 0.5967 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10028 Z= 0.234 Angle : 0.818 14.211 13675 Z= 0.393 Chirality : 0.045 0.308 1584 Planarity : 0.005 0.060 1706 Dihedral : 5.918 54.230 1354 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.21 % Favored : 92.15 % Rotamer: Outliers : 4.39 % Allowed : 28.94 % Favored : 66.67 % 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: -0.36 (0.24), residues: 1235 helix: 1.40 (0.19), residues: 715 sheet: -2.33 (0.41), residues: 127 loop : -2.65 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.050 0.002 PHE B 456 TYR 0.019 0.001 TYR B 225 ARG 0.005 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 235 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.103 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: A 253 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: A 259 MET cc_start: 0.8375 (mmm) cc_final: 0.7953 (tpt) REVERT: A 305 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8907 (tt0) REVERT: A 362 PHE cc_start: 0.9017 (t80) cc_final: 0.8692 (t80) REVERT: B 210 MET cc_start: 0.9246 (mmm) cc_final: 0.8752 (mmt) REVERT: B 441 PHE cc_start: 0.8400 (m-80) cc_final: 0.8145 (m-80) REVERT: C 218 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (m-10) outliers start: 46 outliers final: 37 residues processed: 214 average time/residue: 0.1680 time to fit residues: 54.7322 Evaluate side-chains 216 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER 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 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE 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 522 LEU Chi-restraints excluded: chain A residue 565 TYR 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 660 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL 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 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 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: 0.5993 moved from start: 0.6154 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= 0.307 Angle : 0.827 13.931 13675 Z= 0.405 Chirality : 0.046 0.323 1584 Planarity : 0.005 0.061 1706 Dihedral : 5.846 58.701 1352 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.69 % Favored : 91.58 % Rotamer: Outliers : 4.20 % Allowed : 29.51 % Favored : 66.28 % 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: -0.48 (0.24), residues: 1235 helix: 1.24 (0.19), residues: 721 sheet: -2.25 (0.42), residues: 120 loop : -2.69 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C 174 HIS 0.005 0.001 HIS A 553 PHE 0.037 0.002 PHE B 456 TYR 0.018 0.002 TYR A 569 ARG 0.005 0.000 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 222 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.217 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: A 253 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 259 MET cc_start: 0.8560 (mmm) cc_final: 0.8193 (tpt) REVERT: A 305 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8889 (tt0) REVERT: B 93 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8976 (mmt) REVERT: B 210 MET cc_start: 0.9333 (mmm) cc_final: 0.8864 (mmt) REVERT: B 441 PHE cc_start: 0.8555 (m-80) cc_final: 0.8307 (m-80) REVERT: C 218 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7972 (m-10) outliers start: 44 outliers final: 37 residues processed: 202 average time/residue: 0.1684 time to fit residues: 51.5327 Evaluate side-chains 210 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 SER 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 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE 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 565 TYR 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 B residue 80 LYS Chi-restraints excluded: chain B residue 93 MET 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 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR 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: 4.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 237 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3371 r_free = 0.3371 target = 0.067664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057122 restraints weight = 49258.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058693 restraints weight = 28418.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059752 restraints weight = 18942.335| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10028 Z= 0.269 Angle : 0.823 14.332 13675 Z= 0.398 Chirality : 0.046 0.337 1584 Planarity : 0.005 0.061 1706 Dihedral : 5.776 58.459 1352 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.29 % Favored : 92.06 % Rotamer: Outliers : 4.11 % Allowed : 30.09 % Favored : 65.81 % 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: -0.54 (0.24), residues: 1235 helix: 1.18 (0.19), residues: 725 sheet: -2.30 (0.40), residues: 127 loop : -2.71 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 PHE 0.033 0.002 PHE B 456 TYR 0.016 0.001 TYR B 225 ARG 0.005 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.62 seconds wall clock time: 38 minutes 48.48 seconds (2328.48 seconds total)