Starting phenix.real_space_refine on Wed Jul 23 10:49:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.map" model { file = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2025/7e39_30977.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1946 2.51 5 N 525 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 3074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 705 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.06, per 1000 atoms: 1.00 Number of scatterers: 3074 At special positions: 0 Unit cell: (56.16, 103.68, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 588 8.00 N 525 7.00 C 1946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 386.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.799A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.173A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.665A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.613A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.210A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.769A pdb=" N MET B 11 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.527A pdb=" N TYR B 49 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.713A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 225 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: 0.79 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1003 1.34 - 1.46: 799 1.46 - 1.58: 1330 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3150 Sorted by residual: bond pdb=" CG LEU A 387 " pdb=" CD1 LEU A 387 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.26e-01 ... (remaining 3145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4093 1.62 - 3.24: 164 3.24 - 4.86: 29 4.86 - 6.48: 3 6.48 - 8.10: 3 Bond angle restraints: 4292 Sorted by residual: angle pdb=" N GLY C 111 " pdb=" CA GLY C 111 " pdb=" C GLY C 111 " ideal model delta sigma weight residual 113.18 118.81 -5.63 2.37e+00 1.78e-01 5.65e+00 angle pdb=" CA TYR B 94 " pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 113.90 109.63 4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" C GLN B 79 " pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 109.26 112.71 -3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" C GLY B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.87 117.62 4.25 1.83e+00 2.99e-01 5.38e+00 angle pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 116.30 124.40 -8.10 3.50e+00 8.16e-02 5.36e+00 ... (remaining 4287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 1588 14.32 - 28.63: 184 28.63 - 42.95: 52 42.95 - 57.26: 12 57.26 - 71.58: 7 Dihedral angle restraints: 1843 sinusoidal: 652 harmonic: 1191 Sorted by residual: dihedral pdb=" CA LEU B 78 " pdb=" C LEU B 78 " pdb=" N GLN B 79 " pdb=" CA GLN B 79 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N GLU B 68 " pdb=" CA GLU B 68 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLN B 79 " pdb=" C GLN B 79 " pdb=" N PRO B 80 " pdb=" CA PRO B 80 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 310 0.041 - 0.083: 104 0.083 - 0.124: 40 0.124 - 0.166: 11 0.166 - 0.207: 1 Chirality restraints: 466 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 43 " pdb=" N VAL B 43 " pdb=" C VAL B 43 " pdb=" CB VAL B 43 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 463 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO B 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " 0.004 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " 0.001 2.00e-02 2.50e+03 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 93 2.68 - 3.24: 3074 3.24 - 3.79: 4685 3.79 - 4.35: 6276 4.35 - 4.90: 10301 Nonbonded interactions: 24429 Sorted by model distance: nonbonded pdb=" NZ LYS B 39 " pdb=" O GLU B 81 " model vdw 2.130 3.120 nonbonded pdb=" OG SER B 63 " pdb=" OG1 THR B 74 " model vdw 2.162 3.040 nonbonded pdb=" NZ LYS B 39 " pdb=" OE2 GLU B 81 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.217 3.120 nonbonded pdb=" O TYR B 49 " pdb=" OG SER B 53 " model vdw 2.225 3.040 ... (remaining 24424 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.005 0.040 3156 Z= 0.215 Angle : 0.776 8.104 4305 Z= 0.421 Chirality : 0.050 0.207 466 Planarity : 0.005 0.057 562 Dihedral : 14.331 71.576 1072 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -3.52 (0.38), residues: 406 helix: -3.93 (0.60), residues: 33 sheet: -1.59 (0.43), residues: 131 loop : -2.63 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 52 HIS 0.005 0.002 HIS A 519 PHE 0.024 0.002 PHE A 456 TYR 0.023 0.002 TYR B 94 ARG 0.003 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 2.14049 ( 3) hydrogen bonds : bond 0.18706 ( 94) hydrogen bonds : angle 9.64269 ( 225) SS BOND : bond 0.00328 ( 5) SS BOND : angle 2.15827 ( 10) covalent geometry : bond 0.00462 ( 3150) covalent geometry : angle 0.76795 ( 4292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.433 Fit side-chains REVERT: A 389 ASP cc_start: 0.7161 (t0) cc_final: 0.6787 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1818 time to fit residues: 8.8576 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 0.0370 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062087 restraints weight = 14323.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063479 restraints weight = 7671.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064391 restraints weight = 4974.061| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3156 Z= 0.175 Angle : 0.678 6.604 4305 Z= 0.354 Chirality : 0.049 0.173 466 Planarity : 0.005 0.058 562 Dihedral : 6.032 24.461 471 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.34 % Allowed : 9.86 % Favored : 89.80 % 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: -3.32 (0.38), residues: 406 helix: -3.76 (0.67), residues: 27 sheet: -1.56 (0.42), residues: 134 loop : -2.49 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.006 0.002 HIS A 519 PHE 0.021 0.002 PHE A 456 TYR 0.020 0.002 TYR B 94 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 1.63650 ( 3) hydrogen bonds : bond 0.03844 ( 94) hydrogen bonds : angle 7.63284 ( 225) SS BOND : bond 0.00248 ( 5) SS BOND : angle 1.54785 ( 10) covalent geometry : bond 0.00390 ( 3150) covalent geometry : angle 0.67337 ( 4292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.356 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1817 time to fit residues: 7.7695 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 50.0000 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.070123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.062886 restraints weight = 14122.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064300 restraints weight = 7549.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065211 restraints weight = 4866.065| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3156 Z= 0.134 Angle : 0.609 6.797 4305 Z= 0.319 Chirality : 0.048 0.189 466 Planarity : 0.005 0.062 562 Dihedral : 5.466 23.648 471 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.38 % Allowed : 12.59 % Favored : 85.03 % 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: -3.01 (0.39), residues: 406 helix: -3.16 (0.94), residues: 21 sheet: -1.38 (0.43), residues: 137 loop : -2.34 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.005 0.002 HIS A 519 PHE 0.023 0.001 PHE A 456 TYR 0.017 0.001 TYR B 94 ARG 0.004 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.75306 ( 3) hydrogen bonds : bond 0.03262 ( 94) hydrogen bonds : angle 7.00051 ( 225) SS BOND : bond 0.00144 ( 5) SS BOND : angle 1.06270 ( 10) covalent geometry : bond 0.00298 ( 3150) covalent geometry : angle 0.60641 ( 4292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.359 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.1644 time to fit residues: 8.2740 Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.070556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063431 restraints weight = 14164.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064871 restraints weight = 7409.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065753 restraints weight = 4683.973| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3156 Z= 0.119 Angle : 0.587 9.179 4305 Z= 0.303 Chirality : 0.047 0.179 466 Planarity : 0.005 0.064 562 Dihedral : 5.089 23.314 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.06 % Allowed : 12.93 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.40), residues: 406 helix: -2.87 (1.03), residues: 21 sheet: -1.17 (0.43), residues: 140 loop : -2.18 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 PHE 0.016 0.001 PHE A 456 TYR 0.018 0.001 TYR B 94 ARG 0.004 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.47129 ( 3) hydrogen bonds : bond 0.02933 ( 94) hydrogen bonds : angle 6.58132 ( 225) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.93406 ( 10) covalent geometry : bond 0.00266 ( 3150) covalent geometry : angle 0.58528 ( 4292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.329 Fit side-chains REVERT: A 365 TYR cc_start: 0.7459 (m-80) cc_final: 0.6831 (m-80) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.1466 time to fit residues: 7.5420 Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062351 restraints weight = 14347.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063766 restraints weight = 7622.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064712 restraints weight = 4889.065| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3156 Z= 0.192 Angle : 0.644 7.929 4305 Z= 0.331 Chirality : 0.048 0.170 466 Planarity : 0.005 0.065 562 Dihedral : 5.467 22.256 471 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.06 % Allowed : 15.31 % Favored : 81.63 % 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: -2.81 (0.40), residues: 406 helix: -2.94 (1.02), residues: 21 sheet: -1.37 (0.42), residues: 148 loop : -2.13 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.005 0.002 HIS A 519 PHE 0.012 0.002 PHE A 377 TYR 0.021 0.002 TYR B 94 ARG 0.004 0.001 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 1.61171 ( 3) hydrogen bonds : bond 0.03201 ( 94) hydrogen bonds : angle 6.70693 ( 225) SS BOND : bond 0.00241 ( 5) SS BOND : angle 1.27118 ( 10) covalent geometry : bond 0.00436 ( 3150) covalent geometry : angle 0.64043 ( 4292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.352 Fit side-chains REVERT: A 365 TYR cc_start: 0.7540 (m-80) cc_final: 0.6902 (m-80) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.1679 time to fit residues: 7.8633 Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063204 restraints weight = 14585.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064656 restraints weight = 7733.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065596 restraints weight = 4935.729| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3156 Z= 0.123 Angle : 0.605 8.093 4305 Z= 0.311 Chirality : 0.047 0.185 466 Planarity : 0.005 0.063 562 Dihedral : 5.154 23.043 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.08 % Allowed : 14.97 % Favored : 80.95 % 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: -2.83 (0.40), residues: 406 helix: -2.88 (1.01), residues: 21 sheet: -1.65 (0.39), residues: 164 loop : -1.92 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.003 0.002 HIS B 91 PHE 0.009 0.001 PHE A 377 TYR 0.013 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.56600 ( 3) hydrogen bonds : bond 0.02915 ( 94) hydrogen bonds : angle 6.44157 ( 225) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.97638 ( 10) covalent geometry : bond 0.00277 ( 3150) covalent geometry : angle 0.60235 ( 4292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.367 Fit side-chains REVERT: A 365 TYR cc_start: 0.7509 (m-80) cc_final: 0.6805 (m-80) REVERT: A 427 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7202 (t0) outliers start: 12 outliers final: 7 residues processed: 39 average time/residue: 0.1392 time to fit residues: 6.9845 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063013 restraints weight = 14361.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064411 restraints weight = 7646.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065360 restraints weight = 4933.305| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3156 Z= 0.143 Angle : 0.601 7.456 4305 Z= 0.311 Chirality : 0.047 0.176 466 Planarity : 0.005 0.064 562 Dihedral : 5.168 24.217 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.10 % Allowed : 15.31 % Favored : 79.59 % 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: -2.74 (0.40), residues: 406 helix: -2.70 (1.04), residues: 21 sheet: -1.57 (0.39), residues: 164 loop : -1.89 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.015 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 1.49880 ( 3) hydrogen bonds : bond 0.03003 ( 94) hydrogen bonds : angle 6.31874 ( 225) SS BOND : bond 0.00176 ( 5) SS BOND : angle 1.03516 ( 10) covalent geometry : bond 0.00324 ( 3150) covalent geometry : angle 0.59874 ( 4292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.331 Fit side-chains REVERT: A 365 TYR cc_start: 0.7504 (m-80) cc_final: 0.6730 (m-80) REVERT: A 427 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7152 (t0) REVERT: A 493 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6490 (tm-30) outliers start: 15 outliers final: 8 residues processed: 41 average time/residue: 0.1313 time to fit residues: 6.9262 Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 20.0000 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 0.0270 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063949 restraints weight = 14334.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.065389 restraints weight = 7590.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066274 restraints weight = 4822.727| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3156 Z= 0.107 Angle : 0.594 8.887 4305 Z= 0.304 Chirality : 0.046 0.183 466 Planarity : 0.004 0.065 562 Dihedral : 4.874 26.458 471 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.40 % Allowed : 17.35 % Favored : 79.25 % 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: -2.55 (0.41), residues: 406 helix: -2.57 (1.06), residues: 21 sheet: -1.46 (0.39), residues: 164 loop : -1.75 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE A 456 TYR 0.013 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 1.43309 ( 3) hydrogen bonds : bond 0.02770 ( 94) hydrogen bonds : angle 6.07616 ( 225) SS BOND : bond 0.00102 ( 5) SS BOND : angle 0.85883 ( 10) covalent geometry : bond 0.00244 ( 3150) covalent geometry : angle 0.59207 ( 4292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7487 (m-80) cc_final: 0.6892 (m-80) REVERT: A 493 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6453 (tm-30) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.1514 time to fit residues: 7.7436 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 0.0060 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064007 restraints weight = 14304.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065446 restraints weight = 7596.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066410 restraints weight = 4830.911| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3156 Z= 0.117 Angle : 0.599 8.701 4305 Z= 0.308 Chirality : 0.046 0.172 466 Planarity : 0.004 0.065 562 Dihedral : 4.798 27.094 471 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.72 % Allowed : 18.03 % Favored : 79.25 % 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: -2.47 (0.41), residues: 406 helix: -2.48 (1.07), residues: 21 sheet: -1.40 (0.40), residues: 164 loop : -1.69 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS B 91 PHE 0.009 0.001 PHE A 377 TYR 0.013 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 1.24255 ( 3) hydrogen bonds : bond 0.02815 ( 94) hydrogen bonds : angle 5.94018 ( 225) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.87932 ( 10) covalent geometry : bond 0.00267 ( 3150) covalent geometry : angle 0.59787 ( 4292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7498 (m-80) cc_final: 0.6889 (m-80) REVERT: A 493 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6431 (tm-30) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.1362 time to fit residues: 6.6170 Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063737 restraints weight = 14099.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065154 restraints weight = 7560.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066111 restraints weight = 4837.562| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3156 Z= 0.130 Angle : 0.621 8.632 4305 Z= 0.320 Chirality : 0.046 0.175 466 Planarity : 0.005 0.065 562 Dihedral : 4.843 26.954 471 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.06 % Allowed : 17.69 % Favored : 79.25 % 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: -2.45 (0.41), residues: 406 helix: -2.41 (1.09), residues: 21 sheet: -1.39 (0.40), residues: 163 loop : -1.68 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.002 HIS B 91 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR B 94 ARG 0.003 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.42786 ( 3) hydrogen bonds : bond 0.02845 ( 94) hydrogen bonds : angle 5.93889 ( 225) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.90953 ( 10) covalent geometry : bond 0.00297 ( 3150) covalent geometry : angle 0.61878 ( 4292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7503 (m-80) cc_final: 0.6873 (m-80) REVERT: A 493 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6433 (tm-30) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.1410 time to fit residues: 6.8686 Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063413 restraints weight = 14183.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064841 restraints weight = 7588.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065786 restraints weight = 4842.779| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3156 Z= 0.145 Angle : 0.638 9.276 4305 Z= 0.330 Chirality : 0.047 0.176 466 Planarity : 0.005 0.064 562 Dihedral : 4.975 26.629 471 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.06 % Allowed : 17.69 % Favored : 79.25 % 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: -2.46 (0.41), residues: 406 helix: -2.35 (1.11), residues: 21 sheet: -1.44 (0.39), residues: 164 loop : -1.66 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.004 0.002 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.016 0.001 TYR B 94 ARG 0.002 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 1.51005 ( 3) hydrogen bonds : bond 0.02928 ( 94) hydrogen bonds : angle 6.01146 ( 225) SS BOND : bond 0.00188 ( 5) SS BOND : angle 1.00684 ( 10) covalent geometry : bond 0.00331 ( 3150) covalent geometry : angle 0.63613 ( 4292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1303.02 seconds wall clock time: 23 minutes 14.15 seconds (1394.15 seconds total)