Starting phenix.real_space_refine on Mon Sep 23 20:15:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/09_2024/7wop_32654.cif" } resolution = 3.51 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= 0.016 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 23 5.16 5 C 3212 2.51 5 N 863 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5107 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.79 Number of scatterers: 5107 At special positions: 0 Unit cell: (86.184, 78.736, 102.144, 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 23 16.00 O 1009 8.00 N 863 7.00 C 3212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " 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: 1.26 Conformation dependent library (CDL) restraints added in 658.7 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1190 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 5.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.830A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.546A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.500A pdb=" N GLU C 84 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.500A pdb=" N HIS C 156 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.502A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 106 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 69 removed outlier: 5.110A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 67 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 177 removed outlier: 5.785A pdb=" N TRP B 173 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG B 164 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 160 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 87 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB1, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.696A pdb=" N TYR C 183 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 174 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1663 1.35 - 1.46: 1355 1.46 - 1.58: 2187 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 5235 Sorted by residual: bond pdb=" N GLY C 237 " pdb=" CA GLY C 237 " ideal model delta sigma weight residual 1.458 1.447 0.011 9.20e-03 1.18e+04 1.34e+00 bond pdb=" CA PRO B 228 " pdb=" C PRO B 228 " ideal model delta sigma weight residual 1.526 1.518 0.008 8.50e-03 1.38e+04 8.29e-01 bond pdb=" C ILE B 226 " pdb=" O ILE B 226 " ideal model delta sigma weight residual 1.232 1.242 -0.010 1.15e-02 7.56e+03 7.95e-01 bond pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 1.514 1.527 -0.012 1.41e-02 5.03e+03 7.51e-01 bond pdb=" N THR B 19 " pdb=" CA THR B 19 " ideal model delta sigma weight residual 1.460 1.470 -0.011 1.42e-02 4.96e+03 5.62e-01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 6811 1.15 - 2.30: 229 2.30 - 3.44: 61 3.44 - 4.59: 12 4.59 - 5.74: 3 Bond angle restraints: 7116 Sorted by residual: angle pdb=" C SER C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.25e+00 angle pdb=" N ASN A 481 " pdb=" CA ASN A 481 " pdb=" C ASN A 481 " ideal model delta sigma weight residual 113.15 109.85 3.30 1.19e+00 7.06e-01 7.69e+00 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.79 110.74 3.05 1.17e+00 7.31e-01 6.81e+00 angle pdb=" N GLY B 95 " pdb=" CA GLY B 95 " pdb=" C GLY B 95 " ideal model delta sigma weight residual 111.36 114.27 -2.91 1.17e+00 7.31e-01 6.17e+00 angle pdb=" N THR B 25 " pdb=" CA THR B 25 " pdb=" C THR B 25 " ideal model delta sigma weight residual 114.09 110.45 3.64 1.55e+00 4.16e-01 5.51e+00 ... (remaining 7111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 2847 16.21 - 32.42: 166 32.42 - 48.63: 36 48.63 - 64.84: 8 64.84 - 81.05: 4 Dihedral angle restraints: 3061 sinusoidal: 1163 harmonic: 1898 Sorted by residual: dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.34 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N TYR B 229 " pdb=" CA TYR B 229 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N PHE B 193 " pdb=" CA PHE B 193 " pdb=" CB PHE B 193 " pdb=" CG PHE B 193 " ideal model delta sinusoidal sigma weight residual 180.00 -120.02 -59.98 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 425 0.029 - 0.057: 221 0.057 - 0.086: 65 0.086 - 0.115: 36 0.115 - 0.143: 6 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA VAL A 483 " pdb=" N VAL A 483 " pdb=" C VAL A 483 " pdb=" CB VAL A 483 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 750 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 7 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 8 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 166 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 167 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO C 7 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.025 5.00e-02 4.00e+02 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 413 2.74 - 3.28: 5253 3.28 - 3.82: 8454 3.82 - 4.36: 9662 4.36 - 4.90: 16798 Nonbonded interactions: 40580 Sorted by model distance: nonbonded pdb=" OG SER B 36 " pdb=" OG SER B 91 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 33 " pdb=" OH TYR C 236 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 27 " pdb=" OD1 ASP C 94 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 159 " model vdw 2.306 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG1 THR B 203 " model vdw 2.328 3.040 ... (remaining 40575 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: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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 : 0.002 0.037 5235 Z= 0.133 Angle : 0.536 5.738 7116 Z= 0.311 Chirality : 0.040 0.143 753 Planarity : 0.004 0.049 932 Dihedral : 10.828 81.052 1847 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 9.21 % Allowed : 8.48 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.81 (0.27), residues: 659 helix: -4.90 (0.33), residues: 26 sheet: -2.57 (0.38), residues: 157 loop : -3.60 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 98 HIS 0.001 0.000 HIS C 159 PHE 0.005 0.001 PHE C 153 TYR 0.006 0.001 TYR B 51 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8461 (m110) cc_final: 0.8186 (m-40) REVERT: A 365 TYR cc_start: 0.8197 (m-80) cc_final: 0.7844 (m-80) REVERT: A 395 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7770 (m) REVERT: A 399 SER cc_start: 0.8050 (m) cc_final: 0.7262 (t) REVERT: A 453 TYR cc_start: 0.7655 (p90) cc_final: 0.7269 (p90) REVERT: A 454 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7978 (tpp-160) REVERT: A 493 ARG cc_start: 0.6932 (ttt180) cc_final: 0.6692 (ttt180) REVERT: B 60 VAL cc_start: 0.6133 (OUTLIER) cc_final: 0.5759 (m) REVERT: B 108 VAL cc_start: 0.6482 (OUTLIER) cc_final: 0.5849 (t) REVERT: B 193 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: C 36 TRP cc_start: 0.7702 (m100) cc_final: 0.7418 (m100) REVERT: C 195 SER cc_start: 0.7910 (p) cc_final: 0.7658 (m) outliers start: 51 outliers final: 19 residues processed: 197 average time/residue: 0.1887 time to fit residues: 46.8319 Evaluate side-chains 162 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 409 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 40 GLN B 129 GLN B 165 GLN B 199 ASN B 202 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 80 GLN C 97 ASN C 137 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5235 Z= 0.233 Angle : 0.646 7.159 7116 Z= 0.334 Chirality : 0.045 0.225 753 Planarity : 0.005 0.049 932 Dihedral : 7.502 56.335 782 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 6.68 % Allowed : 16.97 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.38 (0.28), residues: 659 helix: -4.10 (0.51), residues: 34 sheet: -1.91 (0.41), residues: 145 loop : -3.42 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 98 HIS 0.005 0.001 HIS B 41 PHE 0.021 0.002 PHE C 192 TYR 0.020 0.002 TYR B 220 ARG 0.004 0.001 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8348 (m-80) cc_final: 0.7853 (m-80) REVERT: A 403 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7525 (mtp-110) REVERT: A 433 VAL cc_start: 0.8463 (t) cc_final: 0.8206 (t) REVERT: A 453 TYR cc_start: 0.7851 (p90) cc_final: 0.7260 (p90) REVERT: A 493 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6795 (ttt180) REVERT: B 60 VAL cc_start: 0.6364 (OUTLIER) cc_final: 0.6066 (m) REVERT: B 185 TYR cc_start: 0.6845 (m-80) cc_final: 0.6616 (m-80) REVERT: B 193 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: B 195 ILE cc_start: 0.7258 (mt) cc_final: 0.6736 (tt) REVERT: B 229 TYR cc_start: 0.7767 (t80) cc_final: 0.7522 (t80) REVERT: C 33 THR cc_start: 0.7655 (p) cc_final: 0.7362 (m) REVERT: C 68 SER cc_start: 0.8641 (t) cc_final: 0.8411 (p) REVERT: C 170 GLU cc_start: 0.7435 (pp20) cc_final: 0.6568 (pp20) REVERT: C 171 TRP cc_start: 0.7665 (t60) cc_final: 0.7226 (t60) REVERT: C 192 PHE cc_start: 0.6858 (m-80) cc_final: 0.6475 (m-10) REVERT: C 236 TYR cc_start: 0.7933 (p90) cc_final: 0.7648 (p90) outliers start: 37 outliers final: 24 residues processed: 179 average time/residue: 0.1648 time to fit residues: 37.9960 Evaluate side-chains 170 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 59 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5235 Z= 0.176 Angle : 0.611 7.467 7116 Z= 0.315 Chirality : 0.045 0.159 753 Planarity : 0.005 0.048 932 Dihedral : 6.990 58.390 777 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 6.50 % Allowed : 20.22 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.29), residues: 659 helix: -3.54 (0.64), residues: 34 sheet: -1.73 (0.40), residues: 156 loop : -3.12 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.031 0.002 PHE C 153 TYR 0.016 0.001 TYR C 236 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8332 (m-80) cc_final: 0.7747 (m-80) REVERT: A 378 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8122 (ttmt) REVERT: A 433 VAL cc_start: 0.8409 (t) cc_final: 0.8191 (t) REVERT: A 453 TYR cc_start: 0.7759 (p90) cc_final: 0.7237 (p90) REVERT: A 454 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7938 (ttm170) REVERT: A 458 LYS cc_start: 0.7910 (tppt) cc_final: 0.7636 (tppt) REVERT: A 493 ARG cc_start: 0.6965 (ttt180) cc_final: 0.6714 (ttt180) REVERT: B 60 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6203 (m) REVERT: B 163 VAL cc_start: 0.8514 (m) cc_final: 0.8208 (p) REVERT: B 193 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: B 195 ILE cc_start: 0.7311 (mt) cc_final: 0.6616 (tt) REVERT: B 227 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6793 (tp-100) REVERT: B 229 TYR cc_start: 0.7733 (t80) cc_final: 0.7530 (t80) REVERT: C 33 THR cc_start: 0.7567 (p) cc_final: 0.7274 (m) REVERT: C 170 GLU cc_start: 0.7581 (pp20) cc_final: 0.6718 (pp20) REVERT: C 171 TRP cc_start: 0.7532 (t60) cc_final: 0.7088 (t60) REVERT: C 236 TYR cc_start: 0.7963 (p90) cc_final: 0.7523 (p90) outliers start: 36 outliers final: 24 residues processed: 172 average time/residue: 0.1812 time to fit residues: 39.3215 Evaluate side-chains 168 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5235 Z= 0.202 Angle : 0.619 6.531 7116 Z= 0.321 Chirality : 0.045 0.142 753 Planarity : 0.005 0.044 932 Dihedral : 7.114 59.102 776 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 7.40 % Allowed : 20.22 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.30), residues: 659 helix: -3.15 (0.72), residues: 34 sheet: -1.51 (0.40), residues: 158 loop : -3.10 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 98 HIS 0.004 0.001 HIS B 41 PHE 0.031 0.002 PHE C 153 TYR 0.021 0.001 TYR B 185 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7148 (ptp-110) cc_final: 0.6908 (ptp-110) REVERT: A 365 TYR cc_start: 0.8303 (m-80) cc_final: 0.7674 (m-80) REVERT: A 378 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8131 (ttmt) REVERT: A 403 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7757 (mtp-110) REVERT: A 423 TYR cc_start: 0.7777 (t80) cc_final: 0.7494 (t80) REVERT: A 433 VAL cc_start: 0.8257 (t) cc_final: 0.8023 (t) REVERT: A 453 TYR cc_start: 0.7806 (p90) cc_final: 0.7356 (p90) REVERT: A 493 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6758 (ttt180) REVERT: B 60 VAL cc_start: 0.6298 (OUTLIER) cc_final: 0.5943 (m) REVERT: B 85 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.4994 (pm20) REVERT: B 185 TYR cc_start: 0.6756 (m-80) cc_final: 0.6375 (m-80) REVERT: B 195 ILE cc_start: 0.7205 (mt) cc_final: 0.6907 (tt) REVERT: B 227 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6693 (tp-100) REVERT: C 33 THR cc_start: 0.7656 (p) cc_final: 0.7329 (m) REVERT: C 170 GLU cc_start: 0.7661 (pp20) cc_final: 0.6866 (pp20) REVERT: C 171 TRP cc_start: 0.7709 (t60) cc_final: 0.7122 (t60) REVERT: C 173 SER cc_start: 0.7588 (t) cc_final: 0.7382 (p) REVERT: C 207 MET cc_start: 0.6515 (mmt) cc_final: 0.6185 (mmt) REVERT: C 236 TYR cc_start: 0.7898 (p90) cc_final: 0.7495 (p90) outliers start: 41 outliers final: 27 residues processed: 175 average time/residue: 0.1749 time to fit residues: 38.9127 Evaluate side-chains 175 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 207 GLN B 209 ASN C 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5235 Z= 0.265 Angle : 0.670 6.278 7116 Z= 0.351 Chirality : 0.047 0.159 753 Planarity : 0.005 0.044 932 Dihedral : 6.956 45.728 772 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 7.22 % Allowed : 20.76 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.30), residues: 659 helix: -2.91 (0.78), residues: 34 sheet: -1.72 (0.40), residues: 166 loop : -3.05 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 98 HIS 0.004 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.034 0.002 TYR B 93 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7127 (ptp-110) cc_final: 0.6785 (ptp-110) REVERT: A 378 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8131 (ttmt) REVERT: A 453 TYR cc_start: 0.7904 (p90) cc_final: 0.7350 (p90) REVERT: A 474 GLN cc_start: 0.7429 (tt0) cc_final: 0.7227 (tt0) REVERT: A 493 ARG cc_start: 0.7012 (ttt180) cc_final: 0.6812 (ttt180) REVERT: B 102 PHE cc_start: 0.8556 (m-80) cc_final: 0.8261 (m-10) REVERT: B 174 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 185 TYR cc_start: 0.6792 (m-80) cc_final: 0.6501 (m-80) REVERT: B 195 ILE cc_start: 0.7394 (mt) cc_final: 0.7011 (tt) REVERT: B 227 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6439 (tp-100) REVERT: B 231 TYR cc_start: 0.6511 (t80) cc_final: 0.6243 (t80) REVERT: C 33 THR cc_start: 0.7638 (p) cc_final: 0.7292 (m) REVERT: C 40 LEU cc_start: 0.8420 (mm) cc_final: 0.8208 (mp) REVERT: C 68 SER cc_start: 0.8675 (t) cc_final: 0.8430 (p) REVERT: C 158 MET cc_start: 0.8305 (mmm) cc_final: 0.8061 (mmp) REVERT: C 170 GLU cc_start: 0.7739 (pp20) cc_final: 0.7285 (pp20) REVERT: C 207 MET cc_start: 0.5800 (mmt) cc_final: 0.5599 (mmm) REVERT: C 236 TYR cc_start: 0.7787 (p90) cc_final: 0.7268 (p90) outliers start: 40 outliers final: 27 residues processed: 180 average time/residue: 0.1723 time to fit residues: 39.6296 Evaluate side-chains 175 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5235 Z= 0.233 Angle : 0.667 6.037 7116 Z= 0.348 Chirality : 0.046 0.147 753 Planarity : 0.005 0.045 932 Dihedral : 6.770 45.532 770 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer: Outliers : 7.22 % Allowed : 20.58 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.30), residues: 659 helix: -3.08 (0.72), residues: 40 sheet: -1.65 (0.40), residues: 168 loop : -3.01 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.045 0.002 TYR B 93 ARG 0.009 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7155 (ptp-110) cc_final: 0.6791 (ptp-110) REVERT: A 365 TYR cc_start: 0.8321 (m-80) cc_final: 0.7729 (m-80) REVERT: A 374 PHE cc_start: 0.7638 (m-10) cc_final: 0.7424 (m-10) REVERT: A 378 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8103 (ttmt) REVERT: A 453 TYR cc_start: 0.7896 (p90) cc_final: 0.7373 (p90) REVERT: A 456 PHE cc_start: 0.8373 (m-80) cc_final: 0.8158 (m-10) REVERT: A 474 GLN cc_start: 0.7450 (tt0) cc_final: 0.6817 (tt0) REVERT: B 25 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6905 (p) REVERT: B 85 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5078 (pm20) REVERT: B 102 PHE cc_start: 0.8480 (m-80) cc_final: 0.8177 (m-10) REVERT: B 174 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8237 (p) REVERT: B 193 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: B 195 ILE cc_start: 0.7378 (mt) cc_final: 0.6982 (tt) REVERT: B 227 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6355 (tp-100) REVERT: B 231 TYR cc_start: 0.6675 (t80) cc_final: 0.6399 (t80) REVERT: C 33 THR cc_start: 0.7600 (p) cc_final: 0.7291 (m) REVERT: C 40 LEU cc_start: 0.8440 (mm) cc_final: 0.8232 (mp) REVERT: C 68 SER cc_start: 0.8679 (t) cc_final: 0.8418 (p) REVERT: C 170 GLU cc_start: 0.7816 (pp20) cc_final: 0.7417 (pp20) REVERT: C 236 TYR cc_start: 0.7665 (p90) cc_final: 0.7251 (p90) outliers start: 40 outliers final: 29 residues processed: 169 average time/residue: 0.1852 time to fit residues: 39.7311 Evaluate side-chains 174 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5235 Z= 0.286 Angle : 0.705 6.278 7116 Z= 0.371 Chirality : 0.048 0.209 753 Planarity : 0.005 0.045 932 Dihedral : 7.037 45.534 770 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 7.22 % Allowed : 20.94 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.30), residues: 659 helix: -3.00 (0.73), residues: 40 sheet: -1.74 (0.40), residues: 162 loop : -3.01 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.044 0.002 TYR B 93 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.6273 (t80) REVERT: A 355 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6771 (tmt90) REVERT: A 357 ARG cc_start: 0.7138 (ptp-110) cc_final: 0.6772 (ptp-110) REVERT: A 378 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8122 (ttmt) REVERT: A 423 TYR cc_start: 0.7767 (t80) cc_final: 0.7510 (t80) REVERT: A 453 TYR cc_start: 0.7973 (p90) cc_final: 0.7361 (p90) REVERT: B 25 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.6919 (p) REVERT: B 85 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5118 (pm20) REVERT: B 111 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4140 (tm) REVERT: B 174 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 185 TYR cc_start: 0.7098 (m-80) cc_final: 0.6683 (m-80) REVERT: B 227 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6397 (tp-100) REVERT: B 231 TYR cc_start: 0.6928 (t80) cc_final: 0.6601 (t80) REVERT: C 33 THR cc_start: 0.7560 (p) cc_final: 0.7275 (m) REVERT: C 68 SER cc_start: 0.8603 (t) cc_final: 0.8349 (p) REVERT: C 100 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: C 158 MET cc_start: 0.8313 (mmm) cc_final: 0.8039 (mmm) REVERT: C 170 GLU cc_start: 0.7796 (pp20) cc_final: 0.7474 (pp20) REVERT: C 236 TYR cc_start: 0.7684 (p90) cc_final: 0.7330 (p90) outliers start: 40 outliers final: 28 residues processed: 168 average time/residue: 0.1788 time to fit residues: 38.0128 Evaluate side-chains 177 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.0000 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5235 Z= 0.310 Angle : 0.733 7.873 7116 Z= 0.387 Chirality : 0.048 0.157 753 Planarity : 0.005 0.046 932 Dihedral : 7.146 45.156 770 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.15 % Favored : 82.85 % Rotamer: Outliers : 7.40 % Allowed : 23.10 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.30), residues: 659 helix: -3.04 (0.71), residues: 40 sheet: -1.78 (0.40), residues: 164 loop : -3.04 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.049 0.002 TYR B 93 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6423 (t80) REVERT: A 350 VAL cc_start: 0.7997 (m) cc_final: 0.7562 (p) REVERT: A 357 ARG cc_start: 0.7064 (ptp-110) cc_final: 0.6691 (ptp-110) REVERT: A 374 PHE cc_start: 0.7769 (m-10) cc_final: 0.7508 (m-10) REVERT: A 378 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: A 453 TYR cc_start: 0.7985 (p90) cc_final: 0.7536 (p90) REVERT: B 25 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6906 (p) REVERT: B 85 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: B 111 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4131 (tm) REVERT: B 174 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 185 TYR cc_start: 0.7481 (m-80) cc_final: 0.7212 (m-80) REVERT: B 195 ILE cc_start: 0.7652 (tt) cc_final: 0.7385 (tt) REVERT: B 227 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6466 (tp-100) REVERT: B 231 TYR cc_start: 0.7080 (t80) cc_final: 0.6763 (t80) REVERT: C 33 THR cc_start: 0.7550 (p) cc_final: 0.7205 (m) REVERT: C 68 SER cc_start: 0.8649 (t) cc_final: 0.8403 (p) REVERT: C 100 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7383 (m-10) REVERT: C 236 TYR cc_start: 0.7689 (p90) cc_final: 0.7412 (p90) outliers start: 41 outliers final: 31 residues processed: 168 average time/residue: 0.1856 time to fit residues: 39.9419 Evaluate side-chains 179 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5235 Z= 0.263 Angle : 0.721 7.034 7116 Z= 0.378 Chirality : 0.047 0.154 753 Planarity : 0.005 0.052 932 Dihedral : 7.065 45.280 770 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 6.86 % Allowed : 24.73 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.30), residues: 659 helix: -3.67 (0.67), residues: 34 sheet: -1.66 (0.39), residues: 172 loop : -2.99 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.047 0.002 TYR B 93 ARG 0.011 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6423 (t80) REVERT: A 350 VAL cc_start: 0.7973 (m) cc_final: 0.7613 (p) REVERT: A 355 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6749 (tmt90) REVERT: A 369 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: A 374 PHE cc_start: 0.7810 (m-10) cc_final: 0.7573 (m-10) REVERT: A 453 TYR cc_start: 0.7941 (p90) cc_final: 0.7316 (p90) REVERT: B 25 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6877 (p) REVERT: B 85 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5183 (pm20) REVERT: B 102 PHE cc_start: 0.8375 (m-80) cc_final: 0.8144 (m-10) REVERT: B 111 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4149 (tm) REVERT: B 174 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 185 TYR cc_start: 0.7429 (m-80) cc_final: 0.7115 (m-80) REVERT: B 195 ILE cc_start: 0.7622 (tt) cc_final: 0.7340 (tt) REVERT: B 208 MET cc_start: 0.3706 (OUTLIER) cc_final: 0.3341 (mpp) REVERT: B 227 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6543 (tp-100) REVERT: C 33 THR cc_start: 0.7459 (p) cc_final: 0.7135 (m) REVERT: C 68 SER cc_start: 0.8700 (t) cc_final: 0.8418 (p) REVERT: C 100 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: C 170 GLU cc_start: 0.7689 (pp20) cc_final: 0.7106 (pp20) outliers start: 38 outliers final: 27 residues processed: 162 average time/residue: 0.1726 time to fit residues: 35.3942 Evaluate side-chains 174 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5235 Z= 0.276 Angle : 0.737 8.006 7116 Z= 0.386 Chirality : 0.048 0.154 753 Planarity : 0.005 0.049 932 Dihedral : 7.057 47.047 769 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 6.68 % Allowed : 25.99 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.30), residues: 659 helix: -3.62 (0.67), residues: 34 sheet: -1.87 (0.38), residues: 185 loop : -2.88 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.049 0.002 TYR B 93 ARG 0.011 0.001 ARG C 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6483 (t80) REVERT: A 350 VAL cc_start: 0.7997 (m) cc_final: 0.7657 (p) REVERT: A 355 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6831 (tmt90) REVERT: A 374 PHE cc_start: 0.7763 (m-10) cc_final: 0.7559 (m-10) REVERT: A 378 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8082 (ttmt) REVERT: A 453 TYR cc_start: 0.7939 (p90) cc_final: 0.7178 (p90) REVERT: A 493 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6805 (ttt180) REVERT: B 25 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6839 (p) REVERT: B 85 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.5177 (pm20) REVERT: B 102 PHE cc_start: 0.8364 (m-80) cc_final: 0.8118 (m-10) REVERT: B 111 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.4114 (tm) REVERT: B 174 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 185 TYR cc_start: 0.7439 (m-80) cc_final: 0.7143 (m-80) REVERT: B 195 ILE cc_start: 0.7605 (tt) cc_final: 0.7342 (tt) REVERT: B 227 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6551 (tp-100) REVERT: C 68 SER cc_start: 0.8705 (t) cc_final: 0.8454 (p) REVERT: C 100 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7359 (m-10) REVERT: C 158 MET cc_start: 0.8318 (mmm) cc_final: 0.8096 (mmp) REVERT: C 170 GLU cc_start: 0.7655 (pp20) cc_final: 0.7061 (pp20) REVERT: C 236 TYR cc_start: 0.7748 (p90) cc_final: 0.7391 (p90) outliers start: 37 outliers final: 26 residues processed: 161 average time/residue: 0.1833 time to fit residues: 37.2028 Evaluate side-chains 166 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 422 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143716 restraints weight = 8272.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148223 restraints weight = 4096.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151070 restraints weight = 2379.863| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5235 Z= 0.254 Angle : 0.731 8.387 7116 Z= 0.381 Chirality : 0.048 0.154 753 Planarity : 0.005 0.047 932 Dihedral : 7.022 49.761 769 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 6.86 % Allowed : 25.09 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.30), residues: 659 helix: -3.52 (0.69), residues: 34 sheet: -1.90 (0.39), residues: 175 loop : -2.79 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.046 0.002 TYR B 93 ARG 0.010 0.001 ARG C 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.90 seconds wall clock time: 34 minutes 6.42 seconds (2046.42 seconds total)