Starting phenix.real_space_refine on Tue Feb 13 12:20:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wik_21684/02_2024/6wik_21684_neut.pdb" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3889 2.51 5 N 1029 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6078 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3293 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.82, per 1000 atoms: 0.63 Number of scatterers: 6078 At special positions: 0 Unit cell: (127.33, 115.56, 83.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1127 8.00 N 1029 7.00 C 3889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 45.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.524A pdb=" N ARG C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.729A pdb=" N TYR A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 86 removed outlier: 3.971A pdb=" N GLY A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.722A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.519A pdb=" N ALA A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 200 Proline residue: A 189 - end of helix removed outlier: 3.507A pdb=" N TYR A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.839A pdb=" N GLN A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.922A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 removed outlier: 3.528A pdb=" N GLY A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 484 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.667A pdb=" N ILE A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.800A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.154A pdb=" N THR C 117 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.809A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 87 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.580A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 211 through 216 removed outlier: 3.685A pdb=" N TYR C 212 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.491A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.773A pdb=" N VAL D 167 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 179 389 hydrogen bonds defined for protein. 1092 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: 1.72 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1392 1.33 - 1.45: 1395 1.45 - 1.57: 3348 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6189 Sorted by residual: bond pdb=" N ILE A 203 " pdb=" CA ILE A 203 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N ILE C 126 " pdb=" CA ILE C 126 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 9.99e+00 bond pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.73e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.35e+00 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.76: 83 105.76 - 112.90: 3405 112.90 - 120.04: 2265 120.04 - 127.18: 2631 127.18 - 134.31: 58 Bond angle restraints: 8442 Sorted by residual: angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 111.43 -8.18 1.05e+00 9.07e-01 6.07e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 109.48 -6.17 8.90e-01 1.26e+00 4.81e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 110.29 -7.04 1.05e+00 9.07e-01 4.50e+01 angle pdb=" N PRO D 144 " pdb=" CA PRO D 144 " pdb=" CB PRO D 144 " ideal model delta sigma weight residual 102.85 110.34 -7.49 1.13e+00 7.83e-01 4.40e+01 angle pdb=" N PRO D 237 " pdb=" CA PRO D 237 " pdb=" CB PRO D 237 " ideal model delta sigma weight residual 103.25 110.18 -6.93 1.05e+00 9.07e-01 4.35e+01 ... (remaining 8437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 3270 16.56 - 33.12: 247 33.12 - 49.69: 58 49.69 - 66.25: 12 66.25 - 82.81: 7 Dihedral angle restraints: 3594 sinusoidal: 1136 harmonic: 2458 Sorted by residual: dihedral pdb=" CA GLY D 27 " pdb=" C GLY D 27 " pdb=" N ALA D 28 " pdb=" CA ALA D 28 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU D 30 " pdb=" C LEU D 30 " pdb=" N VAL D 31 " pdb=" CA VAL D 31 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL D 161 " pdb=" C VAL D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 596 0.061 - 0.121: 273 0.121 - 0.182: 108 0.182 - 0.242: 30 0.242 - 0.303: 1 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR D 121 " pdb=" N TYR D 121 " pdb=" C TYR D 121 " pdb=" CB TYR D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 110 " pdb=" N THR D 110 " pdb=" C THR D 110 " pdb=" CB THR D 110 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL D 112 " pdb=" N VAL D 112 " pdb=" C VAL D 112 " pdb=" CB VAL D 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1005 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C GLU A 165 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 166 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 364 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ARG A 364 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 364 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 365 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 63 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO C 64 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.031 5.00e-02 4.00e+02 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 153 2.64 - 3.21: 6067 3.21 - 3.77: 9202 3.77 - 4.34: 11554 4.34 - 4.90: 19877 Nonbonded interactions: 46853 Sorted by model distance: nonbonded pdb=" O ASN A 549 " pdb=" ND2 ASN A 549 " model vdw 2.078 2.520 nonbonded pdb=" O CYS A 387 " pdb=" OG SER A 390 " model vdw 2.254 2.440 nonbonded pdb=" O PHE A 114 " pdb=" OD2 ASP A 118 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 379 " pdb=" OG SER A 382 " model vdw 2.304 2.440 nonbonded pdb=" O LEU A 322 " pdb=" CD1 LEU A 322 " model vdw 2.315 3.460 ... (remaining 46848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.990 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.070 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.012 0.086 6189 Z= 0.801 Angle : 1.274 8.804 8442 Z= 0.933 Chirality : 0.080 0.303 1008 Planarity : 0.005 0.056 1070 Dihedral : 13.633 82.811 2016 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 2.24 % Allowed : 10.48 % Favored : 87.28 % Rotamer: Outliers : 2.55 % Allowed : 16.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.88 (0.26), residues: 849 helix: -2.15 (0.25), residues: 354 sheet: -1.58 (0.36), residues: 188 loop : -3.58 (0.29), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 69 HIS 0.008 0.002 HIS A 116 PHE 0.021 0.002 PHE D 126 TYR 0.018 0.002 TYR C 111 ARG 0.015 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 285 time to evaluate : 0.646 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: D 74 ASN cc_start: 0.6497 (p0) cc_final: 0.6236 (p0) REVERT: A 44 PHE cc_start: 0.8550 (t80) cc_final: 0.8163 (t80) REVERT: A 112 MET cc_start: 0.8045 (mmm) cc_final: 0.7716 (tmm) REVERT: A 119 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8704 (tp30) REVERT: A 297 ASP cc_start: 0.9226 (m-30) cc_final: 0.8660 (m-30) REVERT: A 299 TRP cc_start: 0.7513 (t60) cc_final: 0.7299 (t60) REVERT: A 312 MET cc_start: 0.8444 (mmm) cc_final: 0.8095 (mmm) REVERT: A 321 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7230 (p) REVERT: A 366 LYS cc_start: 0.8560 (tttt) cc_final: 0.7946 (tptt) REVERT: A 393 MET cc_start: 0.8798 (mtt) cc_final: 0.8552 (mpp) REVERT: A 474 ASP cc_start: 0.8918 (t0) cc_final: 0.8607 (t0) REVERT: A 504 LEU cc_start: 0.9246 (mm) cc_final: 0.8710 (mm) outliers start: 14 outliers final: 2 residues processed: 292 average time/residue: 0.1931 time to fit residues: 72.3701 Evaluate side-chains 197 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN A 141 ASN A 144 ASN A 494 ASN A 498 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6189 Z= 0.239 Angle : 0.777 11.816 8442 Z= 0.394 Chirality : 0.044 0.196 1008 Planarity : 0.004 0.029 1070 Dihedral : 4.713 27.247 911 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.01 % Favored : 93.17 % Rotamer: Outliers : 6.92 % Allowed : 27.14 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.63 (0.28), residues: 849 helix: 0.20 (0.26), residues: 378 sheet: -1.00 (0.36), residues: 187 loop : -2.85 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 69 HIS 0.009 0.003 HIS A 536 PHE 0.030 0.002 PHE A 460 TYR 0.016 0.002 TYR D 121 ARG 0.006 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 0.693 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 42 TRP cc_start: 0.9111 (t-100) cc_final: 0.8878 (t-100) REVERT: A 112 MET cc_start: 0.8095 (mmm) cc_final: 0.7778 (tmm) REVERT: A 119 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8660 (tp30) REVERT: A 299 TRP cc_start: 0.7606 (t60) cc_final: 0.7208 (t60) REVERT: A 366 LYS cc_start: 0.8527 (tttt) cc_final: 0.7961 (tptt) REVERT: A 393 MET cc_start: 0.8795 (mtt) cc_final: 0.8586 (mpp) REVERT: A 474 ASP cc_start: 0.8825 (t0) cc_final: 0.8562 (t0) REVERT: A 508 HIS cc_start: 0.8396 (t70) cc_final: 0.8099 (t-90) REVERT: A 534 MET cc_start: 0.8711 (mtm) cc_final: 0.8436 (ttp) REVERT: A 538 MET cc_start: 0.8781 (ttp) cc_final: 0.8490 (ttp) outliers start: 38 outliers final: 26 residues processed: 231 average time/residue: 0.1683 time to fit residues: 50.8816 Evaluate side-chains 207 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6189 Z= 0.210 Angle : 0.705 9.878 8442 Z= 0.356 Chirality : 0.042 0.179 1008 Planarity : 0.004 0.035 1070 Dihedral : 4.252 20.001 907 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.36 % Favored : 92.82 % Rotamer: Outliers : 6.56 % Allowed : 29.51 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.52 (0.29), residues: 849 helix: 1.25 (0.27), residues: 374 sheet: -0.43 (0.37), residues: 195 loop : -2.53 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 158 HIS 0.008 0.002 HIS A 536 PHE 0.013 0.001 PHE C 91 TYR 0.020 0.002 TYR A 502 ARG 0.004 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 0.736 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 299 TRP cc_start: 0.7637 (t60) cc_final: 0.7266 (t60) REVERT: A 309 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7696 (mm) REVERT: A 366 LYS cc_start: 0.8515 (tttt) cc_final: 0.7988 (tptt) REVERT: A 467 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8298 (mmm-85) REVERT: A 474 ASP cc_start: 0.8844 (t0) cc_final: 0.8568 (t0) REVERT: A 508 HIS cc_start: 0.8457 (t70) cc_final: 0.8182 (t70) REVERT: A 538 MET cc_start: 0.8823 (ttp) cc_final: 0.8590 (ttp) outliers start: 36 outliers final: 29 residues processed: 215 average time/residue: 0.1745 time to fit residues: 48.8420 Evaluate side-chains 205 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 40.0000 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 6189 Z= 0.369 Angle : 0.754 9.645 8442 Z= 0.397 Chirality : 0.044 0.163 1008 Planarity : 0.004 0.035 1070 Dihedral : 4.458 20.531 907 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.48 % Favored : 92.70 % Rotamer: Outliers : 10.56 % Allowed : 28.60 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.50 (0.29), residues: 849 helix: 1.06 (0.26), residues: 376 sheet: -0.12 (0.39), residues: 189 loop : -2.41 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 127 HIS 0.012 0.003 HIS A 536 PHE 0.017 0.002 PHE A 473 TYR 0.024 0.002 TYR D 99 ARG 0.005 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7448 (m) REVERT: A 309 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7747 (mm) REVERT: A 312 MET cc_start: 0.8348 (mmm) cc_final: 0.7995 (mmm) REVERT: A 366 LYS cc_start: 0.8520 (tttt) cc_final: 0.8053 (tptt) REVERT: A 474 ASP cc_start: 0.8902 (t0) cc_final: 0.8647 (t0) REVERT: A 508 HIS cc_start: 0.8538 (t70) cc_final: 0.8029 (t70) REVERT: A 511 MET cc_start: 0.8804 (mmm) cc_final: 0.8127 (mmm) REVERT: A 534 MET cc_start: 0.8846 (mtm) cc_final: 0.8453 (ttp) REVERT: A 538 MET cc_start: 0.8842 (ttp) cc_final: 0.8571 (ttp) outliers start: 58 outliers final: 48 residues processed: 208 average time/residue: 0.1657 time to fit residues: 45.3460 Evaluate side-chains 226 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6189 Z= 0.367 Angle : 0.762 8.868 8442 Z= 0.398 Chirality : 0.043 0.145 1008 Planarity : 0.004 0.041 1070 Dihedral : 4.443 19.663 907 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.48 % Favored : 92.58 % Rotamer: Outliers : 9.65 % Allowed : 32.42 % Favored : 57.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.45 (0.29), residues: 849 helix: 1.04 (0.26), residues: 376 sheet: -0.01 (0.38), residues: 191 loop : -2.38 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 69 HIS 0.011 0.003 HIS A 536 PHE 0.013 0.002 PHE A 473 TYR 0.029 0.002 TYR D 99 ARG 0.005 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 LEU cc_start: 0.7676 (tp) cc_final: 0.7150 (tt) REVERT: D 101 GLN cc_start: 0.6187 (tp40) cc_final: 0.5879 (tp40) REVERT: A 309 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 319 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8124 (tmm) REVERT: A 366 LYS cc_start: 0.8526 (tttt) cc_final: 0.8036 (tptt) REVERT: A 474 ASP cc_start: 0.8847 (t0) cc_final: 0.8614 (t0) REVERT: A 508 HIS cc_start: 0.8468 (t70) cc_final: 0.7759 (t70) REVERT: A 534 MET cc_start: 0.8875 (mtm) cc_final: 0.8643 (ttt) REVERT: A 538 MET cc_start: 0.8766 (ttp) cc_final: 0.8522 (ttp) outliers start: 53 outliers final: 41 residues processed: 205 average time/residue: 0.1652 time to fit residues: 44.9231 Evaluate side-chains 210 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6189 Z= 0.305 Angle : 0.742 10.141 8442 Z= 0.384 Chirality : 0.042 0.149 1008 Planarity : 0.004 0.042 1070 Dihedral : 4.468 19.749 907 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.12 % Favored : 93.05 % Rotamer: Outliers : 8.93 % Allowed : 34.79 % Favored : 56.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.28 (0.29), residues: 849 helix: 1.21 (0.26), residues: 375 sheet: -0.04 (0.37), residues: 191 loop : -2.22 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 69 HIS 0.011 0.003 HIS A 536 PHE 0.011 0.001 PHE A 473 TYR 0.026 0.002 TYR D 99 ARG 0.004 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 LEU cc_start: 0.7673 (tp) cc_final: 0.7153 (tt) REVERT: D 101 GLN cc_start: 0.5882 (tp40) cc_final: 0.5619 (tp40) REVERT: A 85 LYS cc_start: 0.8657 (pttt) cc_final: 0.8340 (mtmt) REVERT: A 165 GLU cc_start: 0.8850 (mp0) cc_final: 0.7302 (mp0) REVERT: A 309 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7661 (mm) REVERT: A 312 MET cc_start: 0.8298 (mmm) cc_final: 0.7926 (mmm) REVERT: A 366 LYS cc_start: 0.8414 (tttt) cc_final: 0.7916 (tptt) REVERT: A 474 ASP cc_start: 0.8839 (t0) cc_final: 0.8596 (t0) REVERT: A 506 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 508 HIS cc_start: 0.8448 (t70) cc_final: 0.7832 (t70) REVERT: A 511 MET cc_start: 0.8888 (mmp) cc_final: 0.8581 (mmm) REVERT: A 534 MET cc_start: 0.8872 (mtm) cc_final: 0.8647 (ttt) REVERT: A 538 MET cc_start: 0.8766 (ttp) cc_final: 0.8502 (ttp) outliers start: 49 outliers final: 39 residues processed: 198 average time/residue: 0.1704 time to fit residues: 44.5760 Evaluate side-chains 214 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6189 Z= 0.219 Angle : 0.691 9.122 8442 Z= 0.353 Chirality : 0.041 0.169 1008 Planarity : 0.003 0.033 1070 Dihedral : 4.286 22.855 907 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.89 % Favored : 93.64 % Rotamer: Outliers : 6.56 % Allowed : 37.34 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.29), residues: 849 helix: 1.51 (0.26), residues: 375 sheet: 0.15 (0.37), residues: 184 loop : -2.01 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 69 HIS 0.011 0.002 HIS A 536 PHE 0.008 0.001 PHE C 118 TYR 0.017 0.001 TYR D 99 ARG 0.007 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 0.691 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: D 36 LEU cc_start: 0.7708 (tp) cc_final: 0.7461 (tt) REVERT: A 85 LYS cc_start: 0.8624 (pttt) cc_final: 0.8340 (mtmt) REVERT: A 309 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7714 (mm) REVERT: A 312 MET cc_start: 0.8190 (mmm) cc_final: 0.7829 (mmm) REVERT: A 366 LYS cc_start: 0.8298 (tttt) cc_final: 0.7791 (tptt) REVERT: A 464 ILE cc_start: 0.9019 (mm) cc_final: 0.8534 (mm) REVERT: A 467 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8161 (mmm-85) REVERT: A 474 ASP cc_start: 0.8851 (t0) cc_final: 0.8600 (t0) REVERT: A 508 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7701 (t70) REVERT: A 511 MET cc_start: 0.8842 (mmp) cc_final: 0.8544 (mmm) REVERT: A 538 MET cc_start: 0.8736 (ttp) cc_final: 0.8464 (ttp) outliers start: 36 outliers final: 29 residues processed: 202 average time/residue: 0.1663 time to fit residues: 44.2371 Evaluate side-chains 206 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6189 Z= 0.300 Angle : 0.729 8.939 8442 Z= 0.378 Chirality : 0.043 0.163 1008 Planarity : 0.004 0.036 1070 Dihedral : 4.380 23.166 907 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.36 % Favored : 93.05 % Rotamer: Outliers : 7.65 % Allowed : 36.98 % Favored : 55.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.29), residues: 849 helix: 1.36 (0.26), residues: 377 sheet: 0.02 (0.36), residues: 193 loop : -2.11 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 299 HIS 0.012 0.003 HIS A 536 PHE 0.012 0.001 PHE A 473 TYR 0.017 0.002 TYR A 133 ARG 0.005 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 LEU cc_start: 0.7682 (tp) cc_final: 0.7479 (tt) REVERT: A 85 LYS cc_start: 0.8639 (pttt) cc_final: 0.8372 (mtmt) REVERT: A 219 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8653 (mm-30) REVERT: A 309 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 312 MET cc_start: 0.8277 (mmm) cc_final: 0.7918 (mmm) REVERT: A 366 LYS cc_start: 0.8098 (tttt) cc_final: 0.7325 (tptt) REVERT: A 464 ILE cc_start: 0.9031 (mm) cc_final: 0.8560 (mm) REVERT: A 467 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8427 (mmm-85) REVERT: A 474 ASP cc_start: 0.8865 (t0) cc_final: 0.8635 (t0) REVERT: A 508 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7660 (t70) REVERT: A 534 MET cc_start: 0.8862 (mtm) cc_final: 0.8459 (ttp) REVERT: A 538 MET cc_start: 0.8781 (ttp) cc_final: 0.8511 (ttp) outliers start: 42 outliers final: 34 residues processed: 196 average time/residue: 0.1720 time to fit residues: 44.2932 Evaluate side-chains 204 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6189 Z= 0.220 Angle : 0.746 9.445 8442 Z= 0.375 Chirality : 0.043 0.179 1008 Planarity : 0.003 0.035 1070 Dihedral : 4.328 21.693 907 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.30 % Favored : 94.23 % Rotamer: Outliers : 6.19 % Allowed : 38.43 % Favored : 55.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.13 (0.30), residues: 849 helix: 1.57 (0.26), residues: 376 sheet: 0.04 (0.37), residues: 187 loop : -1.94 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 299 HIS 0.010 0.002 HIS A 536 PHE 0.008 0.001 PHE C 118 TYR 0.016 0.001 TYR A 133 ARG 0.005 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8642 (pttt) cc_final: 0.8378 (mtmt) REVERT: A 219 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8580 (mm-30) REVERT: A 309 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7629 (mm) REVERT: A 312 MET cc_start: 0.8183 (mmm) cc_final: 0.7832 (mmm) REVERT: A 366 LYS cc_start: 0.7562 (tttt) cc_final: 0.7040 (tptt) REVERT: A 464 ILE cc_start: 0.9022 (mm) cc_final: 0.8583 (mm) REVERT: A 467 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: A 474 ASP cc_start: 0.8862 (t0) cc_final: 0.8619 (t0) REVERT: A 508 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7587 (t70) REVERT: A 538 MET cc_start: 0.8820 (ttp) cc_final: 0.8505 (ttp) outliers start: 34 outliers final: 29 residues processed: 197 average time/residue: 0.1597 time to fit residues: 41.7099 Evaluate side-chains 204 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6189 Z= 0.276 Angle : 0.773 10.191 8442 Z= 0.390 Chirality : 0.043 0.179 1008 Planarity : 0.004 0.067 1070 Dihedral : 4.427 21.796 907 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.12 % Favored : 93.52 % Rotamer: Outliers : 6.38 % Allowed : 38.43 % Favored : 55.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.29), residues: 849 helix: 1.44 (0.26), residues: 376 sheet: -0.04 (0.36), residues: 193 loop : -2.06 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 299 HIS 0.011 0.002 HIS A 536 PHE 0.033 0.002 PHE A 460 TYR 0.016 0.001 TYR A 133 ARG 0.009 0.001 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8633 (pttt) cc_final: 0.8379 (mtmt) REVERT: A 219 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8646 (mm-30) REVERT: A 309 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 312 MET cc_start: 0.8247 (mmm) cc_final: 0.7896 (mmm) REVERT: A 366 LYS cc_start: 0.7655 (tttt) cc_final: 0.7250 (tptt) REVERT: A 464 ILE cc_start: 0.9030 (mm) cc_final: 0.8588 (mm) REVERT: A 467 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8119 (mmm-85) REVERT: A 474 ASP cc_start: 0.8880 (t0) cc_final: 0.8639 (t0) REVERT: A 508 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7620 (t70) REVERT: A 534 MET cc_start: 0.8775 (mtm) cc_final: 0.8386 (ttp) REVERT: A 538 MET cc_start: 0.8834 (ttp) cc_final: 0.8531 (ttp) outliers start: 35 outliers final: 31 residues processed: 185 average time/residue: 0.1688 time to fit residues: 41.2061 Evaluate side-chains 202 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068035 restraints weight = 20843.760| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.93 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6189 Z= 0.294 Angle : 0.794 9.720 8442 Z= 0.400 Chirality : 0.043 0.159 1008 Planarity : 0.004 0.037 1070 Dihedral : 4.507 21.723 907 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.60 % Favored : 93.05 % Rotamer: Outliers : 6.19 % Allowed : 38.98 % Favored : 54.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.29), residues: 849 helix: 1.42 (0.26), residues: 370 sheet: -0.06 (0.37), residues: 192 loop : -2.04 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 299 HIS 0.011 0.003 HIS A 536 PHE 0.010 0.001 PHE A 473 TYR 0.016 0.002 TYR A 133 ARG 0.008 0.001 ARG D 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.32 seconds wall clock time: 30 minutes 6.33 seconds (1806.33 seconds total)