Starting phenix.real_space_refine on Fri Jul 25 17:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661.map" model { file = "/net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uwc_42661/07_2025/8uwc_42661_trim.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 16 5.16 5 C 2459 2.51 5 N 655 2.21 5 O 816 1.98 5 H 3821 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 7767 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7656 Classifications: {'peptide': 494} Link IDs: {'PCIS': 5, 'PTRANS': 22, 'TRANS': 466} Chain breaks: 4 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 111 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 97} Link IDs: {None: 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.16, per 1000 atoms: 0.66 Number of scatterers: 7767 At special positions: 0 Unit cell: (69.372, 84.87, 90.774, 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 16 16.00 O 816 8.00 N 655 7.00 C 2459 6.00 H 3821 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 501 " distance=2.04 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 NAG-ASN " NAG A1101 " - " ASN A 515 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 605.2 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 7 sheets defined 29.4% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.506A pdb=" N GLY A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.916A pdb=" N LEU A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 412 through 431 removed outlier: 4.032A pdb=" N ALA A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.556A pdb=" N GLN A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.958A pdb=" N GLN A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 4.714A pdb=" N TYR A 54 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N VAL A 51 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N PHE A 133 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU A 53 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N LYS A 131 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 55 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 removed outlier: 7.479A pdb=" N ILE A 274 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 214 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 275 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 216 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG A 213 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN A 305 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 215 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 304 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA A 335 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU A 306 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 391 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 401 Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 485 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.737A pdb=" N ASP A 533 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 167 hydrogen bonds defined for protein. 453 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: 3.02 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3821 1.04 - 1.23: 392 1.23 - 1.43: 1283 1.43 - 1.63: 2234 1.63 - 1.83: 28 Bond restraints: 7758 Sorted by residual: bond pdb=" CA ASN A 91 " pdb=" CB ASN A 91 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.75e-02 3.27e+03 5.78e+00 bond pdb=" CB CYS A 407 " pdb=" SG CYS A 407 " ideal model delta sigma weight residual 1.808 1.746 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.47e+00 bond pdb=" N THR A 42 " pdb=" CA THR A 42 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 ... (remaining 7753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 12975 1.33 - 2.66: 953 2.66 - 3.99: 71 3.99 - 5.33: 20 5.33 - 6.66: 3 Bond angle restraints: 14022 Sorted by residual: angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" C VAL A 45 " ideal model delta sigma weight residual 106.53 110.77 -4.24 1.41e+00 5.03e-01 9.04e+00 angle pdb=" C LEU A 298 " pdb=" N LYS A 299 " pdb=" CA LYS A 299 " ideal model delta sigma weight residual 120.31 124.83 -4.52 1.52e+00 4.33e-01 8.85e+00 angle pdb=" C ILE A 123 " pdb=" N LYS A 124 " pdb=" CA LYS A 124 " ideal model delta sigma weight residual 120.44 124.29 -3.85 1.36e+00 5.41e-01 8.00e+00 angle pdb=" CA TYR A 561 " pdb=" CB TYR A 561 " pdb=" CG TYR A 561 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 7.00e+00 angle pdb=" CG ARG A 408 " pdb=" CD ARG A 408 " pdb=" NE ARG A 408 " ideal model delta sigma weight residual 112.00 116.81 -4.81 2.20e+00 2.07e-01 4.78e+00 ... (remaining 14017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3270 17.96 - 35.92: 268 35.92 - 53.88: 106 53.88 - 71.84: 32 71.84 - 89.80: 10 Dihedral angle restraints: 3686 sinusoidal: 2010 harmonic: 1676 Sorted by residual: dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 160.98 -67.98 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CA SER A 550 " pdb=" C SER A 550 " pdb=" N TYR A 551 " pdb=" CA TYR A 551 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N ILE A 528 " pdb=" CA ILE A 528 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 3683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 307 0.034 - 0.069: 167 0.069 - 0.103: 87 0.103 - 0.137: 40 0.137 - 0.172: 3 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB THR A 286 " pdb=" CA THR A 286 " pdb=" OG1 THR A 286 " pdb=" CG2 THR A 286 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A 106 " pdb=" N ILE A 106 " pdb=" C ILE A 106 " pdb=" CB ILE A 106 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 601 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " -0.023 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 56 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 575 " 0.024 2.00e-02 2.50e+03 8.75e-03 3.06e+00 pdb=" CG TRP A 575 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 575 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 575 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 575 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 575 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 575 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 575 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 575 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 575 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 575 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 575 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 575 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 575 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 575 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 575 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 237 " 0.018 2.00e-02 2.50e+03 7.91e-03 2.50e+00 pdb=" CG TRP A 237 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 237 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 237 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 237 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 237 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 237 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 237 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 237 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 237 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 237 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 237 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 237 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 237 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 237 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 237 " 0.002 2.00e-02 2.50e+03 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 177 2.08 - 2.71: 13013 2.71 - 3.34: 23457 3.34 - 3.97: 31647 3.97 - 4.60: 48559 Nonbonded interactions: 116853 Sorted by model distance: nonbonded pdb=" HE2 HIS A 225 " pdb=" O GLY A 402 " model vdw 1.446 2.450 nonbonded pdb="HH22 ARG A 134 " pdb=" OD1 ASP A 218 " model vdw 1.477 2.450 nonbonded pdb=" OD1 ASP A 467 " pdb=" H ARG A 470 " model vdw 1.563 2.450 nonbonded pdb=" O ALA A 194 " pdb=" H ALA A 199 " model vdw 1.579 2.450 nonbonded pdb=" HH TYR A 56 " pdb=" OE1 GLN A 110 " model vdw 1.611 2.450 ... (remaining 116848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.150 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.110 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.008 0.062 3940 Z= 0.362 Angle : 0.891 6.657 5355 Z= 0.499 Chirality : 0.054 0.172 604 Planarity : 0.005 0.033 682 Dihedral : 15.703 89.798 1441 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.67 % Allowed : 14.59 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.36), residues: 484 helix: -0.50 (0.43), residues: 121 sheet: -0.41 (0.50), residues: 102 loop : -1.62 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 575 HIS 0.007 0.002 HIS A 225 PHE 0.015 0.003 PHE A 228 TYR 0.028 0.004 TYR A 56 ARG 0.010 0.001 ARG A 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 1) link_NAG-ASN : angle 4.65761 ( 3) hydrogen bonds : bond 0.19356 ( 151) hydrogen bonds : angle 9.39841 ( 453) SS BOND : bond 0.01143 ( 2) SS BOND : angle 2.38065 ( 4) covalent geometry : bond 0.00759 ( 3937) covalent geometry : angle 0.88222 ( 5348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 2.1240 time to fit residues: 139.5824 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.145087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.130210 restraints weight = 19259.779| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.33 r_work: 0.3903 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3940 Z= 0.160 Angle : 0.611 4.458 5355 Z= 0.322 Chirality : 0.049 0.152 604 Planarity : 0.004 0.030 682 Dihedral : 7.815 59.408 558 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.83 % Allowed : 16.75 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.38), residues: 484 helix: 0.65 (0.47), residues: 125 sheet: -0.52 (0.47), residues: 117 loop : -1.31 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 237 HIS 0.007 0.002 HIS A 225 PHE 0.009 0.001 PHE A 293 TYR 0.015 0.002 TYR A 63 ARG 0.007 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 2.40109 ( 3) hydrogen bonds : bond 0.04568 ( 151) hydrogen bonds : angle 6.35184 ( 453) SS BOND : bond 0.00617 ( 2) SS BOND : angle 1.14138 ( 4) covalent geometry : bond 0.00355 ( 3937) covalent geometry : angle 0.60804 ( 5348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.6979 (ptm) cc_final: 0.6679 (ptm) outliers start: 16 outliers final: 4 residues processed: 62 average time/residue: 2.3452 time to fit residues: 150.9212 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 541 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 = 0.4170 r_free = 0.4170 target = 0.143089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.128725 restraints weight = 19509.355| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.29 r_work: 0.3870 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3940 Z= 0.168 Angle : 0.587 5.120 5355 Z= 0.307 Chirality : 0.048 0.143 604 Planarity : 0.004 0.039 682 Dihedral : 6.621 59.193 552 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 19.62 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.38), residues: 484 helix: 0.90 (0.47), residues: 125 sheet: -0.23 (0.48), residues: 111 loop : -1.32 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 237 HIS 0.008 0.001 HIS A 225 PHE 0.010 0.001 PHE A 549 TYR 0.011 0.002 TYR A 63 ARG 0.006 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 2.22081 ( 3) hydrogen bonds : bond 0.04384 ( 151) hydrogen bonds : angle 5.98793 ( 453) SS BOND : bond 0.00681 ( 2) SS BOND : angle 1.02450 ( 4) covalent geometry : bond 0.00370 ( 3937) covalent geometry : angle 0.58472 ( 5348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7786 (mt) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 2.2643 time to fit residues: 131.9875 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.142616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.128177 restraints weight = 19423.278| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.31 r_work: 0.3869 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3940 Z= 0.166 Angle : 0.587 6.074 5355 Z= 0.304 Chirality : 0.047 0.142 604 Planarity : 0.004 0.034 682 Dihedral : 5.933 59.375 552 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.83 % Allowed : 18.90 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.38), residues: 484 helix: 1.00 (0.47), residues: 124 sheet: -0.36 (0.45), residues: 121 loop : -1.25 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.008 0.001 HIS A 225 PHE 0.009 0.001 PHE A 549 TYR 0.010 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 2.05200 ( 3) hydrogen bonds : bond 0.04131 ( 151) hydrogen bonds : angle 5.77112 ( 453) SS BOND : bond 0.00702 ( 2) SS BOND : angle 1.02266 ( 4) covalent geometry : bond 0.00368 ( 3937) covalent geometry : angle 0.58459 ( 5348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7796 (mt) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 1.7515 time to fit residues: 103.1243 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.141453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.126869 restraints weight = 19645.767| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.33 r_work: 0.3849 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3940 Z= 0.209 Angle : 0.622 7.885 5355 Z= 0.322 Chirality : 0.048 0.152 604 Planarity : 0.004 0.034 682 Dihedral : 5.912 59.571 552 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.83 % Allowed : 19.62 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.38), residues: 484 helix: 0.81 (0.46), residues: 125 sheet: -0.46 (0.45), residues: 121 loop : -1.29 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.009 0.001 HIS A 225 PHE 0.010 0.002 PHE A 549 TYR 0.009 0.002 TYR A 56 ARG 0.006 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 2.34098 ( 3) hydrogen bonds : bond 0.04405 ( 151) hydrogen bonds : angle 5.81035 ( 453) SS BOND : bond 0.00918 ( 2) SS BOND : angle 1.19541 ( 4) covalent geometry : bond 0.00462 ( 3937) covalent geometry : angle 0.61939 ( 5348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7822 (mt) REVERT: A 580 GLN cc_start: 0.7686 (mt0) cc_final: 0.7209 (mt0) outliers start: 16 outliers final: 9 residues processed: 54 average time/residue: 1.8135 time to fit residues: 102.8505 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.128011 restraints weight = 19538.489| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.34 r_work: 0.3864 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3940 Z= 0.153 Angle : 0.583 8.348 5355 Z= 0.297 Chirality : 0.047 0.140 604 Planarity : 0.004 0.032 682 Dihedral : 5.660 59.226 552 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.59 % Allowed : 19.62 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.38), residues: 484 helix: 1.05 (0.46), residues: 125 sheet: -0.46 (0.45), residues: 121 loop : -1.19 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.007 0.001 PHE A 549 TYR 0.008 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.98912 ( 3) hydrogen bonds : bond 0.03905 ( 151) hydrogen bonds : angle 5.60464 ( 453) SS BOND : bond 0.00635 ( 2) SS BOND : angle 0.94201 ( 4) covalent geometry : bond 0.00340 ( 3937) covalent geometry : angle 0.58098 ( 5348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7401 (t0) REVERT: A 272 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7749 (mt) outliers start: 15 outliers final: 7 residues processed: 54 average time/residue: 1.8045 time to fit residues: 102.2890 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 541 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 = 0.4168 r_free = 0.4168 target = 0.142583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.127908 restraints weight = 19632.285| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.36 r_work: 0.3866 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3940 Z= 0.148 Angle : 0.584 9.770 5355 Z= 0.295 Chirality : 0.047 0.139 604 Planarity : 0.004 0.032 682 Dihedral : 5.583 59.027 552 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.63 % Allowed : 19.62 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.38), residues: 484 helix: 1.14 (0.47), residues: 125 sheet: -0.44 (0.45), residues: 121 loop : -1.11 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.007 0.001 PHE A 549 TYR 0.008 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.93986 ( 3) hydrogen bonds : bond 0.03789 ( 151) hydrogen bonds : angle 5.53027 ( 453) SS BOND : bond 0.00667 ( 2) SS BOND : angle 0.84544 ( 4) covalent geometry : bond 0.00330 ( 3937) covalent geometry : angle 0.58258 ( 5348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7375 (t0) REVERT: A 272 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 580 GLN cc_start: 0.7640 (mt0) cc_final: 0.7069 (mt0) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 1.9749 time to fit residues: 103.4631 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.127066 restraints weight = 19722.019| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.35 r_work: 0.3859 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3940 Z= 0.173 Angle : 0.608 9.889 5355 Z= 0.308 Chirality : 0.047 0.144 604 Planarity : 0.004 0.032 682 Dihedral : 5.647 59.371 552 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.11 % Allowed : 19.14 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.39), residues: 484 helix: 1.07 (0.47), residues: 125 sheet: -0.43 (0.46), residues: 121 loop : -1.11 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.008 0.001 HIS A 225 PHE 0.008 0.001 PHE A 549 TYR 0.008 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.93131 ( 3) hydrogen bonds : bond 0.03964 ( 151) hydrogen bonds : angle 5.56493 ( 453) SS BOND : bond 0.00703 ( 2) SS BOND : angle 0.99492 ( 4) covalent geometry : bond 0.00388 ( 3937) covalent geometry : angle 0.60604 ( 5348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7774 (mt) outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 1.7792 time to fit residues: 95.4842 Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126769 restraints weight = 19841.925| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.39 r_work: 0.3846 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3940 Z= 0.168 Angle : 0.603 10.031 5355 Z= 0.305 Chirality : 0.047 0.142 604 Planarity : 0.004 0.031 682 Dihedral : 5.668 59.635 552 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 20.10 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.38), residues: 484 helix: 1.07 (0.47), residues: 125 sheet: -0.40 (0.46), residues: 119 loop : -1.06 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.008 0.001 PHE A 549 TYR 0.011 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 1.96603 ( 3) hydrogen bonds : bond 0.03909 ( 151) hydrogen bonds : angle 5.53886 ( 453) SS BOND : bond 0.00656 ( 2) SS BOND : angle 0.94772 ( 4) covalent geometry : bond 0.00375 ( 3937) covalent geometry : angle 0.60134 ( 5348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7757 (mt) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 1.7632 time to fit residues: 87.0363 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.141746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127131 restraints weight = 19743.010| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.38 r_work: 0.3853 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3940 Z= 0.156 Angle : 0.601 9.433 5355 Z= 0.303 Chirality : 0.047 0.140 604 Planarity : 0.004 0.031 682 Dihedral : 5.601 59.750 552 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 19.86 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.39), residues: 484 helix: 1.13 (0.47), residues: 125 sheet: -0.38 (0.46), residues: 119 loop : -0.99 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.007 0.001 PHE A 549 TYR 0.010 0.001 TYR A 63 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 1) link_NAG-ASN : angle 1.86706 ( 3) hydrogen bonds : bond 0.03825 ( 151) hydrogen bonds : angle 5.48870 ( 453) SS BOND : bond 0.00688 ( 2) SS BOND : angle 0.86144 ( 4) covalent geometry : bond 0.00352 ( 3937) covalent geometry : angle 0.59923 ( 5348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7761 (mt) REVERT: A 510 MET cc_start: 0.7655 (mpp) cc_final: 0.7410 (mpp) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 1.7822 time to fit residues: 89.9407 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.126871 restraints weight = 19605.419| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.36 r_work: 0.3849 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3940 Z= 0.162 Angle : 0.601 9.445 5355 Z= 0.304 Chirality : 0.047 0.142 604 Planarity : 0.004 0.032 682 Dihedral : 5.631 59.994 552 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.39 % Allowed : 19.62 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.39), residues: 484 helix: 1.11 (0.47), residues: 125 sheet: -0.39 (0.46), residues: 119 loop : -1.01 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 237 HIS 0.007 0.001 HIS A 225 PHE 0.008 0.001 PHE A 549 TYR 0.010 0.001 TYR A 63 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.90205 ( 3) hydrogen bonds : bond 0.03858 ( 151) hydrogen bonds : angle 5.49587 ( 453) SS BOND : bond 0.00697 ( 2) SS BOND : angle 0.90037 ( 4) covalent geometry : bond 0.00365 ( 3937) covalent geometry : angle 0.59956 ( 5348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8143.79 seconds wall clock time: 138 minutes 28.69 seconds (8308.69 seconds total)