Starting phenix.real_space_refine on Mon Mar 11 11:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et7_28587/03_2024/8et7_28587_trim_updated.pdb" } resolution = 3.77 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= 0.003 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 2698 2.51 5 N 670 2.21 5 O 707 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8111 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8064 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'2PM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.42, per 1000 atoms: 0.54 Number of scatterers: 8111 At special positions: 0 Unit cell: (112.32, 56.16, 73.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 707 8.00 N 670 7.00 C 2698 6.00 H 4007 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 71 " Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 941.1 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.501A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 53 through 61 removed outlier: 4.178A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.572A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 145 through 165 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.588A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 4.174A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 Processing helix chain 'A' and resid 261 through 280 Proline residue: A 271 - end of helix removed outlier: 3.784A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 315 through 319 removed outlier: 4.180A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 375 through 400 removed outlier: 4.316A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 4.303A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.747A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 490 removed outlier: 4.014A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.857A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.049A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 232 hydrogen bonds defined for protein. 636 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: 2.78 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3998 1.03 - 1.23: 12 1.23 - 1.42: 1766 1.42 - 1.62: 2401 1.62 - 1.81: 43 Bond restraints: 8220 Sorted by residual: bond pdb=" C15 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.448 1.512 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C14 2PM A 601 " pdb=" C15 2PM A 601 " ideal model delta sigma weight residual 1.513 1.572 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C16 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.446 1.504 -0.058 2.00e-02 2.50e+03 8.28e+00 bond pdb=" C17 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.446 1.492 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 8215 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 104 106.00 - 113.00: 9481 113.00 - 120.00: 2417 120.00 - 127.00: 2759 127.00 - 134.00: 63 Bond angle restraints: 14824 Sorted by residual: angle pdb=" N VAL A 212 " pdb=" CA VAL A 212 " pdb=" C VAL A 212 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C15 2PM A 601 " pdb=" N1 2PM A 601 " pdb=" C16 2PM A 601 " ideal model delta sigma weight residual 112.87 108.18 4.69 3.00e+00 1.11e-01 2.44e+00 angle pdb=" N CYS A 281 " pdb=" CA CYS A 281 " pdb=" C CYS A 281 " ideal model delta sigma weight residual 110.97 112.63 -1.66 1.09e+00 8.42e-01 2.31e+00 angle pdb=" N GLU A 386 " pdb=" CA GLU A 386 " pdb=" C GLU A 386 " ideal model delta sigma weight residual 111.69 113.52 -1.83 1.23e+00 6.61e-01 2.20e+00 angle pdb=" N ILE A 461 " pdb=" CA ILE A 461 " pdb=" C ILE A 461 " ideal model delta sigma weight residual 109.34 112.37 -3.03 2.08e+00 2.31e-01 2.13e+00 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3621 17.24 - 34.48: 211 34.48 - 51.71: 74 51.71 - 68.95: 33 68.95 - 86.19: 2 Dihedral angle restraints: 3941 sinusoidal: 2085 harmonic: 1856 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 60.20 32.80 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -113.35 27.35 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CA LEU A 23 " pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " pdb=" CD1 LEU A 23 " ideal model delta sinusoidal sigma weight residual 180.00 129.98 50.02 3 1.50e+01 4.44e-03 8.85e+00 ... (remaining 3938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 430 0.025 - 0.051: 158 0.051 - 0.076: 58 0.076 - 0.102: 20 0.102 - 0.127: 8 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 71 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 671 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO A 283 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 71 " -0.012 2.00e-02 2.50e+03 9.96e-03 1.49e+00 pdb=" CG ASN A 71 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 71 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 71 " 0.007 2.00e-02 2.50e+03 pdb="HD21 ASN A 71 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 480 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 481 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.016 5.00e-02 4.00e+02 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 749 2.24 - 2.83: 17913 2.83 - 3.42: 21013 3.42 - 4.01: 27324 4.01 - 4.60: 42227 Nonbonded interactions: 109226 Sorted by model distance: nonbonded pdb=" O ILE A 305 " pdb="HD22 ASN A 309 " model vdw 1.650 1.850 nonbonded pdb=" OE1 GLN A 342 " pdb=" H GLN A 342 " model vdw 1.683 1.850 nonbonded pdb=" O ARG A 90 " pdb=" H GLY A 119 " model vdw 1.766 1.850 nonbonded pdb=" H ARG A 175 " pdb=" OE2 GLU A 284 " model vdw 1.771 1.850 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.785 1.850 ... (remaining 109221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.140 Extract box with map and model: 2.250 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 31.250 Find NCS groups from input model: 0.150 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 0.064 4213 Z= 0.213 Angle : 0.493 4.908 5749 Z= 0.259 Chirality : 0.034 0.127 674 Planarity : 0.003 0.031 709 Dihedral : 11.060 86.190 1481 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.24 % Allowed : 5.19 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.38), residues: 530 helix: 2.32 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 275 TYR 0.012 0.001 TYR A 240 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 0.652 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 19 LYS cc_start: 0.8206 (mttt) cc_final: 0.7456 (mtmm) REVERT: A 45 THR cc_start: 0.9113 (m) cc_final: 0.8737 (p) REVERT: A 70 LEU cc_start: 0.8765 (tp) cc_final: 0.8520 (tp) REVERT: A 209 GLN cc_start: 0.8718 (tt0) cc_final: 0.8462 (tt0) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3000 time to fit residues: 69.1766 Evaluate side-chains 125 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4213 Z= 0.177 Angle : 0.543 4.730 5749 Z= 0.289 Chirality : 0.034 0.120 674 Planarity : 0.005 0.035 709 Dihedral : 5.188 38.953 620 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 13.44 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.37), residues: 530 helix: 2.08 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.77 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.005 0.002 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.012 0.001 TYR A 240 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9229 (m) cc_final: 0.8774 (p) REVERT: A 342 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7190 (mm-40) REVERT: A 347 THR cc_start: 0.7873 (m) cc_final: 0.7428 (m) REVERT: A 364 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 11 outliers final: 6 residues processed: 128 average time/residue: 0.2470 time to fit residues: 42.2950 Evaluate side-chains 117 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 510 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS A 367 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4213 Z= 0.267 Angle : 0.575 5.311 5749 Z= 0.318 Chirality : 0.035 0.127 674 Planarity : 0.005 0.034 709 Dihedral : 5.328 39.081 620 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.54 % Allowed : 15.09 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.37), residues: 530 helix: 1.73 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.12 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.008 0.002 HIS A 367 PHE 0.011 0.001 PHE A 275 TYR 0.015 0.002 TYR A 240 ARG 0.003 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9213 (m) cc_final: 0.8814 (p) REVERT: A 364 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 479 ILE cc_start: 0.9232 (tp) cc_final: 0.8951 (tt) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.2513 time to fit residues: 40.0898 Evaluate side-chains 121 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4213 Z= 0.209 Angle : 0.538 4.725 5749 Z= 0.291 Chirality : 0.034 0.124 674 Planarity : 0.004 0.035 709 Dihedral : 5.220 37.689 620 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.77 % Allowed : 17.22 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.37), residues: 530 helix: 1.80 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.99 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.007 0.001 HIS A 367 PHE 0.011 0.001 PHE A 275 TYR 0.016 0.001 TYR A 240 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9207 (m) cc_final: 0.8823 (p) REVERT: A 364 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (tt) outliers start: 16 outliers final: 15 residues processed: 125 average time/residue: 0.2486 time to fit residues: 41.4196 Evaluate side-chains 124 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4213 Z= 0.280 Angle : 0.580 4.760 5749 Z= 0.323 Chirality : 0.035 0.132 674 Planarity : 0.005 0.034 709 Dihedral : 5.467 38.383 620 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.72 % Allowed : 16.98 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.37), residues: 530 helix: 1.49 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.006 0.001 HIS A 367 PHE 0.011 0.001 PHE A 391 TYR 0.015 0.002 TYR A 72 ARG 0.003 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9230 (m) cc_final: 0.8900 (p) REVERT: A 364 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8541 (tt) outliers start: 20 outliers final: 18 residues processed: 123 average time/residue: 0.2649 time to fit residues: 42.6070 Evaluate side-chains 128 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 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 297 GLN A 367 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4213 Z= 0.164 Angle : 0.529 4.790 5749 Z= 0.281 Chirality : 0.034 0.156 674 Planarity : 0.004 0.035 709 Dihedral : 5.220 37.077 620 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.25 % Allowed : 19.34 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.38), residues: 530 helix: 1.76 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.18 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS A 123 PHE 0.011 0.001 PHE A 275 TYR 0.026 0.002 TYR A 72 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9250 (m) cc_final: 0.8911 (p) REVERT: A 364 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8508 (tt) outliers start: 18 outliers final: 16 residues processed: 119 average time/residue: 0.2932 time to fit residues: 46.5562 Evaluate side-chains 125 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4213 Z= 0.240 Angle : 0.563 4.965 5749 Z= 0.309 Chirality : 0.035 0.150 674 Planarity : 0.005 0.049 709 Dihedral : 5.368 38.084 620 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.72 % Allowed : 18.63 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.37), residues: 530 helix: 1.58 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.004 0.001 HIS A 123 PHE 0.010 0.001 PHE A 275 TYR 0.021 0.002 TYR A 72 ARG 0.004 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9236 (m) cc_final: 0.8926 (p) REVERT: A 233 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7479 (ttp-110) REVERT: A 364 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8461 (tt) outliers start: 20 outliers final: 18 residues processed: 121 average time/residue: 0.2666 time to fit residues: 42.3633 Evaluate side-chains 124 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4213 Z= 0.150 Angle : 0.515 4.622 5749 Z= 0.271 Chirality : 0.033 0.136 674 Planarity : 0.004 0.036 709 Dihedral : 5.005 36.846 620 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.54 % Allowed : 19.58 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.38), residues: 530 helix: 1.89 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.12 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 123 PHE 0.011 0.001 PHE A 275 TYR 0.018 0.001 TYR A 72 ARG 0.005 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9214 (m) cc_final: 0.8895 (p) REVERT: A 364 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8504 (tt) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.2672 time to fit residues: 41.6701 Evaluate side-chains 120 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4213 Z= 0.197 Angle : 0.527 4.738 5749 Z= 0.285 Chirality : 0.034 0.135 674 Planarity : 0.004 0.036 709 Dihedral : 5.084 37.930 620 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.30 % Allowed : 19.81 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.38), residues: 530 helix: 1.83 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.07 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 429 HIS 0.003 0.001 HIS A 123 PHE 0.010 0.001 PHE A 275 TYR 0.020 0.001 TYR A 72 ARG 0.004 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9269 (m) cc_final: 0.8951 (p) REVERT: A 86 ARG cc_start: 0.8598 (tmt170) cc_final: 0.8297 (ttp80) REVERT: A 364 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 14 outliers final: 13 residues processed: 115 average time/residue: 0.2739 time to fit residues: 41.0998 Evaluate side-chains 119 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4213 Z= 0.147 Angle : 0.506 4.678 5749 Z= 0.267 Chirality : 0.033 0.130 674 Planarity : 0.004 0.043 709 Dihedral : 4.891 37.196 620 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.30 % Allowed : 19.34 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.39), residues: 530 helix: 2.04 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.05 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 146 HIS 0.003 0.001 HIS A 123 PHE 0.011 0.001 PHE A 275 TYR 0.018 0.001 TYR A 72 ARG 0.007 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9255 (m) cc_final: 0.8939 (p) REVERT: A 86 ARG cc_start: 0.8600 (tmt170) cc_final: 0.8296 (ttp80) REVERT: A 364 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (tt) outliers start: 14 outliers final: 13 residues processed: 117 average time/residue: 0.2480 time to fit residues: 38.3476 Evaluate side-chains 122 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144577 restraints weight = 18514.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150395 restraints weight = 7089.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154007 restraints weight = 3684.889| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4213 Z= 0.159 Angle : 0.511 4.704 5749 Z= 0.270 Chirality : 0.033 0.128 674 Planarity : 0.004 0.036 709 Dihedral : 4.847 37.519 620 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.07 % Allowed : 19.81 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 530 helix: 2.09 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.08 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 288 HIS 0.003 0.001 HIS A 48 PHE 0.010 0.001 PHE A 275 TYR 0.017 0.001 TYR A 72 ARG 0.001 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.26 seconds wall clock time: 45 minutes 58.77 seconds (2758.77 seconds total)