Starting phenix.real_space_refine on Sat Jul 26 03:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_28587_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_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/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_28587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_28587.map" model { file = "/net/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_28587_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et7_28587/07_2025/8et7_28587_trim.cif" } 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.44, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 71 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 732.1 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... Secondary structure from input PDB file: 28 helices and 1 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 32 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) Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.003A pdb=" N GLY A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.979A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) 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) removed outlier: 4.050A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.659A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.572A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 4.174A pdb=" N ALA A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 145 through 166 removed outlier: 4.369A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.618A pdb=" N ALA A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.720A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 198 through 228 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 232 through 258 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.784A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.678A pdb=" N LEU A 317 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.911A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.186A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) 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 403 through 423 Processing helix chain 'A' and resid 428 through 457 removed outlier: 3.896A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 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 493 through 510 removed outlier: 3.637A pdb=" N ILE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.682A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 264 hydrogen bonds defined for protein. 777 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: 3.19 Time building geometry restraints manager: 2.82 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: 0.00 - 0.98: 13569 0.98 - 1.96: 1183 1.96 - 2.95: 44 2.95 - 3.93: 18 3.93 - 4.91: 10 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: 3622 17.24 - 34.48: 211 34.48 - 51.71: 74 51.71 - 68.95: 33 68.95 - 86.19: 2 Dihedral angle restraints: 3942 sinusoidal: 2086 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 3939 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=" 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 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.016 5.00e-02 4.00e+02 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 719 2.24 - 2.83: 17899 2.83 - 3.42: 20994 3.42 - 4.01: 27283 4.01 - 4.60: 42172 Nonbonded interactions: 109067 Sorted by model distance: nonbonded pdb=" O ILE A 305 " pdb="HD22 ASN A 309 " model vdw 1.650 2.450 nonbonded pdb=" OE1 GLN A 342 " pdb=" H GLN A 342 " model vdw 1.683 2.450 nonbonded pdb=" O ARG A 90 " pdb=" H GLY A 119 " model vdw 1.766 2.450 nonbonded pdb=" H ARG A 175 " pdb=" OE2 GLU A 284 " model vdw 1.771 2.450 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.785 2.450 ... (remaining 109062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.160 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- 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 4218 Z= 0.160 Angle : 0.505 5.614 5761 Z= 0.262 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 1) link_NAG-ASN : angle 4.20562 ( 3) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 1.90629 ( 3) hydrogen bonds : bond 0.14986 ( 264) hydrogen bonds : angle 5.57493 ( 777) SS BOND : bond 0.00312 ( 3) SS BOND : angle 1.12026 ( 6) covalent geometry : bond 0.00318 ( 4213) covalent geometry : angle 0.49269 ( 5749) *********************** 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 to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.618 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: 0.3009 time to fit residues: 69.9538 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.176770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151818 restraints weight = 18438.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158204 restraints weight = 7283.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162072 restraints weight = 3805.704| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4218 Z= 0.150 Angle : 0.564 4.731 5761 Z= 0.300 Chirality : 0.035 0.122 674 Planarity : 0.004 0.035 709 Dihedral : 5.154 39.063 620 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.73 % 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: 1.79 (0.37), residues: 530 helix: 2.14 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.85 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 491 HIS 0.004 0.001 HIS A 367 PHE 0.019 0.002 PHE A 275 TYR 0.012 0.001 TYR A 240 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 2.28296 ( 3) link_BETA1-4 : bond 0.00483 ( 1) link_BETA1-4 : angle 1.63492 ( 3) hydrogen bonds : bond 0.05903 ( 264) hydrogen bonds : angle 4.75779 ( 777) SS BOND : bond 0.00336 ( 3) SS BOND : angle 1.52305 ( 6) covalent geometry : bond 0.00308 ( 4213) covalent geometry : angle 0.55835 ( 5749) *********************** 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 139 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 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: A 45 THR cc_start: 0.9260 (m) cc_final: 0.8854 (p) REVERT: A 347 THR cc_start: 0.8088 (m) cc_final: 0.7752 (m) REVERT: A 364 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.2501 time to fit residues: 45.0319 Evaluate side-chains 123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 155 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 346 HIS A 367 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148307 restraints weight = 18908.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154429 restraints weight = 7421.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158155 restraints weight = 3911.229| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4218 Z= 0.173 Angle : 0.571 4.615 5761 Z= 0.307 Chirality : 0.035 0.126 674 Planarity : 0.005 0.054 709 Dihedral : 5.221 38.621 620 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.07 % Allowed : 13.68 % Favored : 83.25 % 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: 1.65 (0.37), residues: 530 helix: 2.09 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.06 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.008 0.002 HIS A 123 PHE 0.016 0.001 PHE A 275 TYR 0.014 0.001 TYR A 240 ARG 0.003 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 2.40729 ( 3) link_BETA1-4 : bond 0.00341 ( 1) link_BETA1-4 : angle 1.57155 ( 3) hydrogen bonds : bond 0.05504 ( 264) hydrogen bonds : angle 4.72007 ( 777) SS BOND : bond 0.00316 ( 3) SS BOND : angle 1.17702 ( 6) covalent geometry : bond 0.00360 ( 4213) covalent geometry : angle 0.56666 ( 5749) *********************** 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 138 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8804 (m-80) cc_final: 0.8567 (m-80) REVERT: A 45 THR cc_start: 0.9227 (m) cc_final: 0.8859 (p) REVERT: A 146 TRP cc_start: 0.8318 (p-90) cc_final: 0.8021 (p90) REVERT: A 193 MET cc_start: 0.8647 (ttp) cc_final: 0.8408 (ttt) REVERT: A 364 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8400 (tt) outliers start: 13 outliers final: 11 residues processed: 131 average time/residue: 0.2372 time to fit residues: 42.0203 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 155 VAL 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 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 411 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146846 restraints weight = 18985.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152882 restraints weight = 7345.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156586 restraints weight = 3835.129| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4218 Z= 0.157 Angle : 0.552 4.856 5761 Z= 0.294 Chirality : 0.034 0.126 674 Planarity : 0.004 0.033 709 Dihedral : 5.137 37.391 620 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.01 % Allowed : 17.22 % Favored : 78.77 % 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: 1.74 (0.38), residues: 530 helix: 2.15 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.03 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.006 0.001 HIS A 367 PHE 0.015 0.001 PHE A 275 TYR 0.015 0.001 TYR A 240 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 2.47439 ( 3) link_BETA1-4 : bond 0.00202 ( 1) link_BETA1-4 : angle 1.60816 ( 3) hydrogen bonds : bond 0.05279 ( 264) hydrogen bonds : angle 4.61632 ( 777) SS BOND : bond 0.00208 ( 3) SS BOND : angle 1.06877 ( 6) covalent geometry : bond 0.00325 ( 4213) covalent geometry : angle 0.54727 ( 5749) *********************** 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 132 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9242 (m) cc_final: 0.8871 (p) REVERT: A 193 MET cc_start: 0.8650 (ttp) cc_final: 0.8430 (ttt) REVERT: A 364 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8361 (tt) outliers start: 17 outliers final: 14 residues processed: 124 average time/residue: 0.2434 time to fit residues: 41.4131 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 155 VAL 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 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.3912 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151048 restraints weight = 18636.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157132 restraints weight = 7199.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160807 restraints weight = 3735.571| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4218 Z= 0.109 Angle : 0.520 4.721 5761 Z= 0.266 Chirality : 0.033 0.125 674 Planarity : 0.004 0.041 709 Dihedral : 4.911 36.440 620 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.30 % Allowed : 18.16 % Favored : 78.54 % 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: 2.06 (0.38), residues: 530 helix: 2.35 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.005 0.001 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.014 0.001 TYR A 240 ARG 0.010 0.001 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 2.22340 ( 3) link_BETA1-4 : bond 0.00342 ( 1) link_BETA1-4 : angle 1.47762 ( 3) hydrogen bonds : bond 0.04665 ( 264) hydrogen bonds : angle 4.21681 ( 777) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.79605 ( 6) covalent geometry : bond 0.00222 ( 4213) covalent geometry : angle 0.51617 ( 5749) *********************** 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 128 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9262 (m) cc_final: 0.8879 (p) REVERT: A 193 MET cc_start: 0.8609 (ttp) cc_final: 0.8369 (ttt) REVERT: A 364 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8377 (tt) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.2412 time to fit residues: 40.8748 Evaluate side-chains 119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 145 SER Chi-restraints excluded: chain A residue 155 VAL 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 386 GLU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.175277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151213 restraints weight = 18642.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157241 restraints weight = 7163.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.160851 restraints weight = 3710.119| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4218 Z= 0.113 Angle : 0.510 4.694 5761 Z= 0.265 Chirality : 0.034 0.127 674 Planarity : 0.004 0.033 709 Dihedral : 4.798 36.690 620 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 18.40 % Favored : 78.54 % 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: 2.16 (0.38), residues: 530 helix: 2.43 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE A 275 TYR 0.013 0.001 TYR A 240 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 2.15491 ( 3) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 1.38081 ( 3) hydrogen bonds : bond 0.04449 ( 264) hydrogen bonds : angle 4.18179 ( 777) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.64418 ( 6) covalent geometry : bond 0.00239 ( 4213) covalent geometry : angle 0.50685 ( 5749) *********************** 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 119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9264 (m) cc_final: 0.8932 (p) REVERT: A 193 MET cc_start: 0.8590 (ttp) cc_final: 0.8348 (ttt) REVERT: A 364 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 455 GLU cc_start: 0.8624 (tp30) cc_final: 0.8386 (tp30) REVERT: A 457 TYR cc_start: 0.8408 (m-80) cc_final: 0.8203 (m-80) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.2267 time to fit residues: 35.8307 Evaluate side-chains 117 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 155 VAL 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 364 LEU Chi-restraints excluded: chain A residue 386 GLU 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 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.175333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151391 restraints weight = 18685.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157413 restraints weight = 7155.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161089 restraints weight = 3688.011| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4218 Z= 0.108 Angle : 0.501 4.713 5761 Z= 0.259 Chirality : 0.034 0.126 674 Planarity : 0.004 0.034 709 Dihedral : 4.684 36.798 620 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.30 % Allowed : 18.40 % 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: 2.20 (0.38), residues: 530 helix: 2.47 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.004 0.001 HIS A 367 PHE 0.011 0.001 PHE A 275 TYR 0.012 0.001 TYR A 72 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 1) link_NAG-ASN : angle 2.05910 ( 3) link_BETA1-4 : bond 0.00353 ( 1) link_BETA1-4 : angle 1.43919 ( 3) hydrogen bonds : bond 0.04285 ( 264) hydrogen bonds : angle 4.08942 ( 777) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.53811 ( 6) covalent geometry : bond 0.00226 ( 4213) covalent geometry : angle 0.49775 ( 5749) *********************** 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 124 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9269 (m) cc_final: 0.8966 (p) REVERT: A 193 MET cc_start: 0.8575 (ttp) cc_final: 0.8338 (ttt) REVERT: A 364 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 455 GLU cc_start: 0.8613 (tp30) cc_final: 0.8404 (tp30) REVERT: A 457 TYR cc_start: 0.8390 (m-80) cc_final: 0.8175 (m-80) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.2369 time to fit residues: 38.9764 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL 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 386 GLU 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 14 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.175570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151457 restraints weight = 19071.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157570 restraints weight = 7305.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161048 restraints weight = 3744.547| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4218 Z= 0.106 Angle : 0.500 4.721 5761 Z= 0.257 Chirality : 0.034 0.126 674 Planarity : 0.004 0.034 709 Dihedral : 4.621 36.768 620 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 19.34 % 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: 2.32 (0.38), residues: 530 helix: 2.56 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.79 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.003 0.001 HIS A 367 PHE 0.011 0.001 PHE A 275 TYR 0.014 0.001 TYR A 240 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 2.03420 ( 3) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 1.26396 ( 3) hydrogen bonds : bond 0.04188 ( 264) hydrogen bonds : angle 4.05939 ( 777) SS BOND : bond 0.00133 ( 3) SS BOND : angle 0.41899 ( 6) covalent geometry : bond 0.00224 ( 4213) covalent geometry : angle 0.49741 ( 5749) *********************** 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 121 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9272 (m) cc_final: 0.8967 (p) REVERT: A 193 MET cc_start: 0.8563 (ttp) cc_final: 0.8306 (ttt) REVERT: A 364 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 457 TYR cc_start: 0.8365 (m-80) cc_final: 0.8135 (m-80) outliers start: 10 outliers final: 9 residues processed: 116 average time/residue: 0.2441 time to fit residues: 39.5350 Evaluate side-chains 121 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 155 VAL 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 364 LEU Chi-restraints excluded: chain A residue 386 GLU 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 10 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 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 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150378 restraints weight = 19279.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156399 restraints weight = 7361.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159963 restraints weight = 3779.224| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4218 Z= 0.114 Angle : 0.504 4.790 5761 Z= 0.261 Chirality : 0.034 0.126 674 Planarity : 0.004 0.034 709 Dihedral : 4.574 36.981 620 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.36 % Allowed : 19.10 % Favored : 78.54 % 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: 2.36 (0.38), residues: 530 helix: 2.60 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.002 0.001 HIS A 123 PHE 0.010 0.001 PHE A 275 TYR 0.013 0.001 TYR A 240 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 2.01619 ( 3) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 1.35791 ( 3) hydrogen bonds : bond 0.04248 ( 264) hydrogen bonds : angle 4.09296 ( 777) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.43453 ( 6) covalent geometry : bond 0.00239 ( 4213) covalent geometry : angle 0.50089 ( 5749) *********************** 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 124 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9285 (m) cc_final: 0.8987 (p) REVERT: A 193 MET cc_start: 0.8541 (ttp) cc_final: 0.8299 (ttt) REVERT: A 364 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 457 TYR cc_start: 0.8349 (m-80) cc_final: 0.8085 (m-80) outliers start: 10 outliers final: 9 residues processed: 119 average time/residue: 0.2846 time to fit residues: 45.4318 Evaluate side-chains 120 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 155 VAL 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 364 LEU Chi-restraints excluded: chain A residue 386 GLU 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 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.174240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149336 restraints weight = 18791.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155463 restraints weight = 7202.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159177 restraints weight = 3719.930| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4218 Z= 0.144 Angle : 0.531 4.907 5761 Z= 0.281 Chirality : 0.034 0.126 674 Planarity : 0.004 0.035 709 Dihedral : 4.656 37.553 620 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.83 % Allowed : 19.34 % Favored : 77.83 % 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: 2.21 (0.38), residues: 530 helix: 2.42 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.80 (0.52), residues: 164 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 0.015 0.002 TYR A 72 ARG 0.004 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 2.12516 ( 3) link_BETA1-4 : bond 0.00260 ( 1) link_BETA1-4 : angle 1.32510 ( 3) hydrogen bonds : bond 0.04627 ( 264) hydrogen bonds : angle 4.26572 ( 777) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.44833 ( 6) covalent geometry : bond 0.00304 ( 4213) covalent geometry : angle 0.52808 ( 5749) ********************** 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 123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9271 (m) cc_final: 0.9000 (p) REVERT: A 193 MET cc_start: 0.8622 (ttp) cc_final: 0.8388 (ttt) REVERT: A 364 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (tt) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.2238 time to fit residues: 36.9047 Evaluate side-chains 118 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 155 VAL 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 364 LEU 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 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.171069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147259 restraints weight = 18804.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153109 restraints weight = 7124.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156650 restraints weight = 3664.181| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4218 Z= 0.121 Angle : 0.517 4.850 5761 Z= 0.269 Chirality : 0.034 0.129 674 Planarity : 0.004 0.037 709 Dihedral : 4.614 37.010 620 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.07 % Allowed : 19.34 % Favored : 77.59 % 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: 2.27 (0.38), residues: 530 helix: 2.43 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.71 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.002 0.001 HIS A 123 PHE 0.011 0.001 PHE A 275 TYR 0.018 0.002 TYR A 91 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 2.08141 ( 3) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 1.35774 ( 3) hydrogen bonds : bond 0.04480 ( 264) hydrogen bonds : angle 4.14584 ( 777) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.38393 ( 6) covalent geometry : bond 0.00254 ( 4213) covalent geometry : angle 0.51454 ( 5749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.29 seconds wall clock time: 64 minutes 29.52 seconds (3869.52 seconds total)