Starting phenix.real_space_refine on Mon Mar 11 17:00:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/03_2024/7tqd_26066_updated.pdb" } resolution = 2.9 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= 0.009 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5503 2.51 5 N 1511 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3999 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 484} Chain breaks: 4 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2961 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'peptide': 357, 'undetermined': 4} Modifications used: {'rna2p': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335, None: 5} Not linked: pdbres="ALA C 381 " pdbres="AMP C 401 " Not linked: pdbres="AMP C 401 " pdbres=" MG C 402 " Not linked: pdbres=" MG C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="ATP C 404 " Not linked: pdbres="ATP C 404 " pdbres="ADP C 405 " Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.17, per 1000 atoms: 0.59 Number of scatterers: 8690 At special positions: 0 Unit cell: (72.24, 100.8, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1640 8.00 N 1511 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 6 sheets defined 35.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.546A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.841A pdb=" N GLN A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 557 through 576 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 129 through 149 Processing helix chain 'B' and resid 179 through 186 Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 374 through 377 No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 557 through 576 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 85 through 99 removed outlier: 4.281A pdb=" N PHE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 332 removed outlier: 3.589A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.919A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 593 through 597 removed outlier: 6.790A pdb=" N SER A 448 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE A 407 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 450 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 39 through 45 Processing sheet with id= C, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.924A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 294 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA B 316 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 354 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 593 through 596 removed outlier: 6.932A pdb=" N SER B 448 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE B 407 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG B 450 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 104 through 107 removed outlier: 7.329A pdb=" N ASP C 121 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP C 71 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 125 through 127 353 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2843 1.34 - 1.46: 1677 1.46 - 1.58: 4328 1.58 - 1.69: 8 1.69 - 1.81: 46 Bond restraints: 8902 Sorted by residual: bond pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.66e+00 bond pdb=" C4 ADP C 405 " pdb=" C5 ADP C 405 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4 AMP C 401 " pdb=" C5 AMP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CG PRO B 251 " pdb=" CD PRO B 251 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.10e+00 bond pdb=" C2' ADP C 405 " pdb=" C3' ADP C 405 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.31e-01 ... (remaining 8897 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.82: 326 106.82 - 115.05: 5348 115.05 - 123.29: 6016 123.29 - 131.53: 381 131.53 - 139.77: 43 Bond angle restraints: 12114 Sorted by residual: angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.12e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" O ALA B 291 " ideal model delta sigma weight residual 119.13 121.16 -2.03 1.00e+00 1.00e+00 4.11e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 118.95 116.36 2.59 1.29e+00 6.01e-01 4.04e+00 angle pdb=" C ILE B 144 " pdb=" N ASP B 145 " pdb=" CA ASP B 145 " ideal model delta sigma weight residual 120.29 117.48 2.81 1.42e+00 4.96e-01 3.93e+00 angle pdb=" O1B ADP C 405 " pdb=" PB ADP C 405 " pdb=" O3B ADP C 405 " ideal model delta sigma weight residual 119.90 114.10 5.80 3.00e+00 1.11e-01 3.74e+00 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5243 34.65 - 69.30: 67 69.30 - 103.95: 1 103.95 - 138.60: 1 138.60 - 173.25: 2 Dihedral angle restraints: 5314 sinusoidal: 2143 harmonic: 3171 Sorted by residual: dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 126.75 173.25 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.14 149.87 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PB ADP C 405 " pdb=" PA ADP C 405 " ideal model delta sinusoidal sigma weight residual -60.00 59.27 -119.27 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 847 0.028 - 0.056: 325 0.056 - 0.084: 74 0.084 - 0.113: 66 0.113 - 0.141: 18 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C2' ADP C 405 " pdb=" C1' ADP C 405 " pdb=" C3' ADP C 405 " pdb=" O2' ADP C 405 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE C 127 " pdb=" N ILE C 127 " pdb=" C ILE C 127 " pdb=" CB ILE C 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1327 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 291 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ALA B 291 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA B 291 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 292 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 290 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ARG B 290 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG B 290 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 291 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 50 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 20 2.55 - 3.14: 6211 3.14 - 3.72: 12782 3.72 - 4.31: 18375 4.31 - 4.90: 31337 Nonbonded interactions: 68725 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 1.960 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP C 71 " pdb="MG MG C 403 " model vdw 2.254 2.170 nonbonded pdb=" O ARG B 468 " pdb=" NZ LYS B 495 " model vdw 2.276 2.520 nonbonded pdb=" OD1 ASN B 374 " pdb=" NH2 ARG B 377 " model vdw 2.314 2.520 ... (remaining 68720 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=0.50 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: 5.410 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: 16.620 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 27.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.003 0.031 8902 Z= 0.200 Angle : 0.520 7.302 12114 Z= 0.262 Chirality : 0.039 0.141 1330 Planarity : 0.004 0.049 1551 Dihedral : 12.102 173.252 3248 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.95 (0.26), residues: 1078 helix: 2.65 (0.26), residues: 402 sheet: 0.52 (0.34), residues: 232 loop : -1.28 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.009 0.001 PHE C 49 TYR 0.007 0.001 TYR C 225 ARG 0.007 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: A 479 ASP cc_start: 0.7808 (t0) cc_final: 0.7472 (t0) REVERT: B 11 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8218 (tp30) REVERT: B 37 LYS cc_start: 0.9298 (mttt) cc_final: 0.8972 (mmmt) REVERT: B 73 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7397 (mmm160) REVERT: B 102 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7811 (tp30) REVERT: B 216 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8924 (mptt) REVERT: B 231 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8117 (pptt) REVERT: B 276 PHE cc_start: 0.7312 (m-80) cc_final: 0.7054 (m-80) REVERT: B 388 SER cc_start: 0.8518 (m) cc_final: 0.8267 (p) REVERT: B 507 GLU cc_start: 0.8605 (tt0) cc_final: 0.8027 (pt0) REVERT: B 527 ARG cc_start: 0.7413 (mmp80) cc_final: 0.5999 (mmm-85) REVERT: C 342 LEU cc_start: 0.8196 (mt) cc_final: 0.7914 (mm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.6258 time to fit residues: 267.6129 Evaluate side-chains 69 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 178 GLN C 8 ASN C 210 GLN C 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8902 Z= 0.208 Angle : 0.568 8.662 12114 Z= 0.273 Chirality : 0.040 0.160 1330 Planarity : 0.004 0.045 1551 Dihedral : 9.007 142.348 1224 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.20 % Allowed : 10.98 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.93 (0.26), residues: 1078 helix: 2.64 (0.26), residues: 402 sheet: 0.48 (0.33), residues: 234 loop : -1.30 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 PHE 0.011 0.001 PHE B 510 TYR 0.007 0.001 TYR A 584 ARG 0.010 0.001 ARG B 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.067 Fit side-chains REVERT: A 377 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7828 (ttp-110) REVERT: A 479 ASP cc_start: 0.7832 (t0) cc_final: 0.7547 (t0) REVERT: A 539 ASP cc_start: 0.7888 (m-30) cc_final: 0.7674 (m-30) REVERT: A 595 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7909 (tttp) REVERT: B 11 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8169 (tp30) REVERT: B 131 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7720 (t0) REVERT: B 150 GLU cc_start: 0.7368 (tp30) cc_final: 0.6708 (tt0) REVERT: B 216 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8915 (mptt) REVERT: B 231 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8120 (pptt) REVERT: B 259 GLN cc_start: 0.8014 (tp40) cc_final: 0.7743 (tp40) REVERT: B 507 GLU cc_start: 0.8568 (tt0) cc_final: 0.8020 (pt0) REVERT: B 527 ARG cc_start: 0.7547 (mmp80) cc_final: 0.6147 (mmm-85) REVERT: C 2 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: C 325 GLU cc_start: 0.8534 (tt0) cc_final: 0.8268 (tp30) outliers start: 20 outliers final: 7 residues processed: 83 average time/residue: 1.4183 time to fit residues: 125.3289 Evaluate side-chains 64 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8902 Z= 0.183 Angle : 0.525 9.822 12114 Z= 0.249 Chirality : 0.039 0.150 1330 Planarity : 0.004 0.037 1551 Dihedral : 8.067 114.535 1224 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 13.17 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.99 (0.26), residues: 1078 helix: 2.68 (0.26), residues: 401 sheet: 0.52 (0.33), residues: 234 loop : -1.24 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.012 0.001 PHE A 510 TYR 0.007 0.001 TYR C 225 ARG 0.004 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 479 ASP cc_start: 0.7839 (t0) cc_final: 0.7515 (t0) REVERT: A 539 ASP cc_start: 0.7802 (m-30) cc_final: 0.7587 (m-30) REVERT: B 11 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8061 (tp30) REVERT: B 150 GLU cc_start: 0.7321 (tp30) cc_final: 0.6662 (tt0) REVERT: B 216 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8931 (mptt) REVERT: B 231 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8233 (pptt) REVERT: B 259 GLN cc_start: 0.8066 (tp40) cc_final: 0.7767 (tp40) REVERT: B 267 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: B 507 GLU cc_start: 0.8588 (tt0) cc_final: 0.8054 (pt0) REVERT: B 527 ARG cc_start: 0.7687 (mmp80) cc_final: 0.6295 (mmm-85) REVERT: B 594 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: C 194 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7258 (pt) outliers start: 18 outliers final: 8 residues processed: 74 average time/residue: 1.4493 time to fit residues: 114.2185 Evaluate side-chains 63 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 237 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8902 Z= 0.225 Angle : 0.556 9.512 12114 Z= 0.265 Chirality : 0.040 0.161 1330 Planarity : 0.004 0.033 1551 Dihedral : 7.506 90.058 1224 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.41 % Allowed : 13.83 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.89 (0.26), residues: 1078 helix: 2.57 (0.26), residues: 403 sheet: 0.51 (0.33), residues: 234 loop : -1.34 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 PHE 0.014 0.002 PHE A 510 TYR 0.008 0.001 TYR C 225 ARG 0.006 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 539 ASP cc_start: 0.7802 (m-30) cc_final: 0.7577 (m-30) REVERT: A 595 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8090 (tttp) REVERT: B 11 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8028 (tp30) REVERT: B 216 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8936 (mptt) REVERT: B 218 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7058 (ttpp) REVERT: B 231 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8565 (ptpp) REVERT: B 259 GLN cc_start: 0.8051 (tp40) cc_final: 0.7611 (tm-30) REVERT: B 267 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: B 507 GLU cc_start: 0.8571 (tt0) cc_final: 0.7951 (pt0) REVERT: B 527 ARG cc_start: 0.7905 (mmp80) cc_final: 0.6492 (mmm-85) REVERT: B 594 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7670 (mm-30) outliers start: 22 outliers final: 11 residues processed: 76 average time/residue: 1.3338 time to fit residues: 108.1390 Evaluate side-chains 69 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 210 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8902 Z= 0.195 Angle : 0.523 10.790 12114 Z= 0.249 Chirality : 0.039 0.149 1330 Planarity : 0.004 0.032 1551 Dihedral : 7.256 84.294 1224 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 14.82 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.94 (0.26), residues: 1078 helix: 2.56 (0.26), residues: 410 sheet: 0.48 (0.34), residues: 232 loop : -1.25 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.007 0.001 TYR C 225 ARG 0.003 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.950 Fit side-chains REVERT: A 539 ASP cc_start: 0.7760 (m-30) cc_final: 0.7550 (m-30) REVERT: A 595 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8137 (tttp) REVERT: B 11 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8017 (tp30) REVERT: B 150 GLU cc_start: 0.7242 (tp30) cc_final: 0.6403 (tt0) REVERT: B 218 LYS cc_start: 0.7334 (ttmt) cc_final: 0.7067 (ttpp) REVERT: B 231 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8615 (ptpp) REVERT: B 259 GLN cc_start: 0.8009 (tp40) cc_final: 0.7583 (tm-30) REVERT: B 267 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: B 507 GLU cc_start: 0.8528 (tt0) cc_final: 0.7889 (pt0) REVERT: B 527 ARG cc_start: 0.7890 (mmp80) cc_final: 0.6493 (mmm-85) REVERT: B 594 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: C 194 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7280 (pt) outliers start: 20 outliers final: 6 residues processed: 72 average time/residue: 1.3242 time to fit residues: 102.0303 Evaluate side-chains 62 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 105 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 227 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8902 Z= 0.155 Angle : 0.518 10.759 12114 Z= 0.242 Chirality : 0.039 0.148 1330 Planarity : 0.003 0.031 1551 Dihedral : 7.074 87.357 1224 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.65 % Allowed : 15.92 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.05 (0.26), residues: 1078 helix: 2.67 (0.26), residues: 408 sheet: 0.49 (0.33), residues: 235 loop : -1.18 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.003 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.006 0.001 TYR C 225 ARG 0.003 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.072 Fit side-chains REVERT: A 539 ASP cc_start: 0.7756 (m-30) cc_final: 0.7552 (m-30) REVERT: B 11 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8013 (tp30) REVERT: B 218 LYS cc_start: 0.7361 (ttmt) cc_final: 0.7119 (ttpp) REVERT: B 231 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8655 (ptpp) REVERT: B 259 GLN cc_start: 0.8007 (tp40) cc_final: 0.7567 (tm-30) REVERT: B 267 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: B 507 GLU cc_start: 0.8466 (tt0) cc_final: 0.7813 (pt0) REVERT: B 527 ARG cc_start: 0.7831 (mmp80) cc_final: 0.6447 (mmm-85) REVERT: B 594 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: C 194 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7223 (pt) outliers start: 15 outliers final: 6 residues processed: 65 average time/residue: 1.3469 time to fit residues: 93.8891 Evaluate side-chains 60 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 227 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8902 Z= 0.204 Angle : 0.535 11.653 12114 Z= 0.253 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.032 1551 Dihedral : 7.035 85.781 1224 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.87 % Allowed : 15.81 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.01 (0.26), residues: 1078 helix: 2.62 (0.26), residues: 408 sheet: 0.51 (0.34), residues: 231 loop : -1.19 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.008 0.001 TYR B 582 ARG 0.002 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 539 ASP cc_start: 0.7743 (m-30) cc_final: 0.7542 (m-30) REVERT: B 11 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7919 (tp30) REVERT: B 218 LYS cc_start: 0.7364 (ttmt) cc_final: 0.7129 (ttpp) REVERT: B 231 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8711 (ptpp) REVERT: B 267 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: B 507 GLU cc_start: 0.8471 (tt0) cc_final: 0.7765 (pt0) REVERT: B 527 ARG cc_start: 0.7880 (mmp80) cc_final: 0.6513 (mmm-85) REVERT: B 594 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: C 194 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7267 (pt) outliers start: 17 outliers final: 9 residues processed: 70 average time/residue: 1.3663 time to fit residues: 103.3853 Evaluate side-chains 65 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 469 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8902 Z= 0.245 Angle : 0.556 11.489 12114 Z= 0.267 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.032 1551 Dihedral : 7.069 82.047 1224 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.87 % Allowed : 15.92 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.92 (0.26), residues: 1078 helix: 2.52 (0.26), residues: 407 sheet: 0.47 (0.34), residues: 231 loop : -1.21 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.014 0.002 PHE A 510 TYR 0.009 0.001 TYR B 582 ARG 0.003 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 539 ASP cc_start: 0.7781 (m-30) cc_final: 0.7578 (m-30) REVERT: B 11 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7959 (tp30) REVERT: B 218 LYS cc_start: 0.7383 (ttmt) cc_final: 0.7123 (ttpp) REVERT: B 267 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: B 507 GLU cc_start: 0.8471 (tt0) cc_final: 0.7748 (pt0) REVERT: B 527 ARG cc_start: 0.7806 (mmp80) cc_final: 0.6287 (mpt-90) REVERT: B 594 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7755 (mm-30) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 1.2449 time to fit residues: 85.7640 Evaluate side-chains 62 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8902 Z= 0.166 Angle : 0.516 11.796 12114 Z= 0.244 Chirality : 0.039 0.144 1330 Planarity : 0.003 0.031 1551 Dihedral : 6.936 86.537 1224 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.32 % Allowed : 16.36 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.05 (0.26), residues: 1078 helix: 2.61 (0.26), residues: 408 sheet: 0.53 (0.34), residues: 231 loop : -1.12 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.012 0.001 TYR B 582 ARG 0.005 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 539 ASP cc_start: 0.7747 (m-30) cc_final: 0.7546 (m-30) REVERT: B 11 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7900 (tp30) REVERT: B 150 GLU cc_start: 0.7188 (tp30) cc_final: 0.6357 (tt0) REVERT: B 218 LYS cc_start: 0.7387 (ttmt) cc_final: 0.7130 (ttpp) REVERT: B 507 GLU cc_start: 0.8453 (tt0) cc_final: 0.7764 (pt0) REVERT: B 527 ARG cc_start: 0.7714 (mmp80) cc_final: 0.6328 (mpt-90) REVERT: B 594 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7736 (mm-30) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 1.3158 time to fit residues: 89.0362 Evaluate side-chains 57 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8902 Z= 0.289 Angle : 0.579 11.307 12114 Z= 0.279 Chirality : 0.041 0.148 1330 Planarity : 0.004 0.032 1551 Dihedral : 7.035 80.714 1224 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.43 % Allowed : 16.47 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.83 (0.26), residues: 1078 helix: 2.33 (0.26), residues: 409 sheet: 0.46 (0.33), residues: 231 loop : -1.18 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.014 0.002 PHE A 510 TYR 0.009 0.001 TYR B 582 ARG 0.004 0.000 ARG C 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 1.067 Fit side-chains REVERT: B 11 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8031 (tp30) REVERT: B 218 LYS cc_start: 0.7353 (ttmt) cc_final: 0.7098 (ttpp) REVERT: B 259 GLN cc_start: 0.7883 (tp40) cc_final: 0.7522 (tm-30) REVERT: B 594 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7741 (mm-30) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 1.2768 time to fit residues: 79.9191 Evaluate side-chains 56 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076915 restraints weight = 16947.645| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.09 r_work: 0.3074 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8902 Z= 0.208 Angle : 0.573 14.831 12114 Z= 0.267 Chirality : 0.040 0.145 1330 Planarity : 0.004 0.032 1551 Dihedral : 6.974 82.238 1224 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.99 % Allowed : 17.34 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.85 (0.26), residues: 1078 helix: 2.34 (0.26), residues: 409 sheet: 0.48 (0.33), residues: 231 loop : -1.15 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.012 0.001 TYR B 582 ARG 0.004 0.000 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3093.38 seconds wall clock time: 55 minutes 51.59 seconds (3351.59 seconds total)