Starting phenix.real_space_refine on Sun Apr 27 01:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.map" model { file = "/net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g5k_51088/04_2025/9g5k_51088.cif" } resolution = 2.87 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= 0.001 sd= 0.054 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 20 5.16 5 C 2674 2.51 5 N 633 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 991 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3035 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 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: 3.82, per 1000 atoms: 0.95 Number of scatterers: 4040 At special positions: 0 Unit cell: (87.15, 80.51, 80.51, 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 20 16.00 O 713 8.00 N 633 7.00 C 2674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 45 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 496.1 milliseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 67.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 77 removed outlier: 4.329A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.694A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 4.182A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.502A pdb=" N ASN A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.699A pdb=" N TYR A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.316A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.667A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 425 removed outlier: 3.881A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.136A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.506A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.384A pdb=" N TYR B 32 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG B 52 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 283 hydrogen bonds defined for protein. 810 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: 1.18 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 878 1.33 - 1.45: 1042 1.45 - 1.57: 2198 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4152 Sorted by residual: bond pdb=" CA GLN B 39 " pdb=" C GLN B 39 " ideal model delta sigma weight residual 1.520 1.476 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" CA ASN A 340 " pdb=" C ASN A 340 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N GLN B 39 " pdb=" CA GLN B 39 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.20e-02 6.94e+03 8.22e+00 bond pdb=" CA ASN A 399 " pdb=" C ASN A 399 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.37e-02 5.33e+03 8.10e+00 bond pdb=" CA PRO B 41 " pdb=" C PRO B 41 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.27e-02 6.20e+03 5.75e+00 ... (remaining 4147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 5510 1.66 - 3.32: 128 3.32 - 4.98: 20 4.98 - 6.63: 2 6.63 - 8.29: 1 Bond angle restraints: 5661 Sorted by residual: angle pdb=" C GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta sigma weight residual 110.24 104.46 5.78 1.46e+00 4.69e-01 1.56e+01 angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 110.80 119.09 -8.29 2.13e+00 2.20e-01 1.52e+01 angle pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 120.79 117.90 2.89 9.70e-01 1.06e+00 8.88e+00 angle pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" C TRP A 94 " ideal model delta sigma weight residual 111.82 115.07 -3.25 1.16e+00 7.43e-01 7.84e+00 angle pdb=" C ALA B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 119.76 116.91 2.85 1.03e+00 9.43e-01 7.68e+00 ... (remaining 5656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2095 16.35 - 32.70: 203 32.70 - 49.04: 67 49.04 - 65.39: 14 65.39 - 81.74: 5 Dihedral angle restraints: 2384 sinusoidal: 887 harmonic: 1497 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.11 33.89 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" C GLN B 39 " pdb=" N GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" N LEU B 11 " pdb=" CA LEU B 11 " pdb=" CB LEU B 11 " pdb=" CG LEU B 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.11 57.11 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 537 0.053 - 0.107: 91 0.107 - 0.160: 13 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 645 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 642 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.112 2.00e-02 2.50e+03 9.32e-02 1.09e+02 pdb=" C7 NAG A 601 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.083 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 40 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA B 40 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA B 40 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 339 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C VAL A 339 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 339 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 340 " -0.009 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1033 2.79 - 3.32: 3914 3.32 - 3.85: 6972 3.85 - 4.37: 8161 4.37 - 4.90: 14160 Nonbonded interactions: 34240 Sorted by model distance: nonbonded pdb=" O MET A 384 " pdb=" OG1 THR A 388 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 415 " pdb=" OG1 THR A 419 " model vdw 2.287 3.040 nonbonded pdb=" O LEU A 177 " pdb=" OG SER A 181 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.333 3.040 nonbonded pdb=" O TRP A 12 " pdb=" OG1 THR A 16 " model vdw 2.367 3.040 ... (remaining 34235 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 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: 4.110 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.820 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: 0.010 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.004 0.049 4154 Z= 0.286 Angle : 0.616 8.292 5666 Z= 0.365 Chirality : 0.043 0.266 645 Planarity : 0.005 0.093 690 Dihedral : 15.279 81.741 1427 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.70 % Allowed : 15.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.37), residues: 501 helix: 1.97 (0.30), residues: 294 sheet: -0.23 (0.60), residues: 53 loop : 0.15 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.008 0.001 PHE A 279 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.02143 ( 1) link_NAG-ASN : angle 4.99903 ( 3) hydrogen bonds : bond 0.17004 ( 277) hydrogen bonds : angle 6.76142 ( 810) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.18964 ( 2) covalent geometry : bond 0.00429 ( 4152) covalent geometry : angle 0.60497 ( 5661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.403 Fit side-chains REVERT: B 89 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6769 (mp0) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 1.1645 time to fit residues: 97.6095 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.142127 restraints weight = 4923.283| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.28 r_work: 0.3425 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4154 Z= 0.184 Angle : 0.626 8.953 5666 Z= 0.326 Chirality : 0.043 0.159 645 Planarity : 0.004 0.034 690 Dihedral : 5.481 56.806 587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.99 % Allowed : 14.32 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.37), residues: 501 helix: 2.12 (0.29), residues: 298 sheet: -0.14 (0.59), residues: 59 loop : 0.23 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.002 PHE A 279 TYR 0.018 0.002 TYR B 113 ARG 0.004 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 1.00673 ( 3) hydrogen bonds : bond 0.05293 ( 277) hydrogen bonds : angle 4.55318 ( 810) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.71715 ( 2) covalent geometry : bond 0.00431 ( 4152) covalent geometry : angle 0.62570 ( 5661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.454 Fit side-chains REVERT: A 78 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.5803 (mpt-90) REVERT: A 349 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6958 (tp) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.1195 time to fit residues: 100.9581 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141601 restraints weight = 4932.691| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.30 r_work: 0.3448 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4154 Z= 0.157 Angle : 0.568 8.174 5666 Z= 0.300 Chirality : 0.042 0.150 645 Planarity : 0.004 0.032 690 Dihedral : 4.450 17.877 582 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.23 % Allowed : 16.20 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.37), residues: 501 helix: 2.19 (0.29), residues: 301 sheet: 0.07 (0.58), residues: 59 loop : 0.30 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.012 0.002 PHE A 439 TYR 0.015 0.002 TYR A 280 ARG 0.004 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 0.90319 ( 3) hydrogen bonds : bond 0.04828 ( 277) hydrogen bonds : angle 4.28928 ( 810) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.52983 ( 2) covalent geometry : bond 0.00358 ( 4152) covalent geometry : angle 0.56744 ( 5661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.461 Fit side-chains REVERT: B 19 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: A 440 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (tp) outliers start: 18 outliers final: 8 residues processed: 89 average time/residue: 1.0049 time to fit residues: 92.9798 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.140699 restraints weight = 4923.937| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.31 r_work: 0.3431 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4154 Z= 0.164 Angle : 0.584 8.224 5666 Z= 0.307 Chirality : 0.042 0.151 645 Planarity : 0.004 0.025 690 Dihedral : 4.529 18.511 582 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.23 % Allowed : 16.90 % Favored : 78.87 % 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: 2.01 (0.37), residues: 501 helix: 2.11 (0.29), residues: 301 sheet: 0.10 (0.58), residues: 59 loop : 0.29 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.013 0.002 PHE A 279 TYR 0.018 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 0.90633 ( 3) hydrogen bonds : bond 0.04785 ( 277) hydrogen bonds : angle 4.26774 ( 810) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.53079 ( 2) covalent geometry : bond 0.00382 ( 4152) covalent geometry : angle 0.58391 ( 5661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.400 Fit side-chains REVERT: B 19 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7084 (ttm-80) REVERT: B 89 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 278 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 440 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (tp) outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 1.0441 time to fit residues: 87.8075 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.142646 restraints weight = 5077.166| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.33 r_work: 0.3440 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4154 Z= 0.145 Angle : 0.558 8.174 5666 Z= 0.293 Chirality : 0.041 0.148 645 Planarity : 0.004 0.025 690 Dihedral : 4.452 18.905 582 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.52 % Allowed : 16.90 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.37), residues: 501 helix: 2.20 (0.29), residues: 300 sheet: 0.30 (0.58), residues: 59 loop : 0.39 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.011 0.001 PHE A 439 TYR 0.018 0.002 TYR A 280 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 0.89781 ( 3) hydrogen bonds : bond 0.04524 ( 277) hydrogen bonds : angle 4.16879 ( 810) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.51944 ( 2) covalent geometry : bond 0.00328 ( 4152) covalent geometry : angle 0.55787 ( 5661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.431 Fit side-chains REVERT: B 19 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7116 (ttm-80) REVERT: A 278 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7069 (tt) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 1.0868 time to fit residues: 100.2872 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.156601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140917 restraints weight = 4891.380| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.20 r_work: 0.3433 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4154 Z= 0.177 Angle : 0.601 8.770 5666 Z= 0.315 Chirality : 0.043 0.154 645 Planarity : 0.004 0.025 690 Dihedral : 4.658 20.162 582 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.69 % Allowed : 16.20 % Favored : 79.11 % 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: 2.00 (0.37), residues: 501 helix: 2.04 (0.29), residues: 300 sheet: 0.26 (0.58), residues: 59 loop : 0.38 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.017 0.002 PHE A 279 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.01194 ( 3) hydrogen bonds : bond 0.04837 ( 277) hydrogen bonds : angle 4.25311 ( 810) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.49443 ( 2) covalent geometry : bond 0.00414 ( 4152) covalent geometry : angle 0.60045 ( 5661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.406 Fit side-chains REVERT: B 19 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7061 (ttm-80) REVERT: A 278 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7179 (tt) REVERT: A 440 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8240 (tp) outliers start: 20 outliers final: 9 residues processed: 84 average time/residue: 1.0888 time to fit residues: 94.8625 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.142033 restraints weight = 4924.617| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.22 r_work: 0.3467 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4154 Z= 0.144 Angle : 0.570 9.151 5666 Z= 0.298 Chirality : 0.041 0.147 645 Planarity : 0.004 0.024 690 Dihedral : 4.528 19.577 582 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.76 % Allowed : 17.61 % Favored : 78.64 % 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: 2.17 (0.37), residues: 501 helix: 2.18 (0.29), residues: 300 sheet: 0.37 (0.58), residues: 59 loop : 0.42 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 94 HIS 0.001 0.000 HIS A 200 PHE 0.011 0.001 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 0.92626 ( 3) hydrogen bonds : bond 0.04447 ( 277) hydrogen bonds : angle 4.13030 ( 810) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.53988 ( 2) covalent geometry : bond 0.00325 ( 4152) covalent geometry : angle 0.56944 ( 5661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.970 Fit side-chains REVERT: B 19 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6960 (ttm-80) REVERT: A 278 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 440 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8223 (tp) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 1.4614 time to fit residues: 131.9268 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.141874 restraints weight = 4841.444| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.21 r_work: 0.3470 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4154 Z= 0.139 Angle : 0.573 9.129 5666 Z= 0.299 Chirality : 0.041 0.148 645 Planarity : 0.004 0.024 690 Dihedral : 4.418 19.251 582 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.99 % Allowed : 17.61 % Favored : 78.40 % 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: 2.23 (0.37), residues: 501 helix: 2.23 (0.29), residues: 300 sheet: 0.44 (0.57), residues: 59 loop : 0.41 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.025 0.002 PHE A 279 TYR 0.020 0.001 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 0.99888 ( 3) hydrogen bonds : bond 0.04346 ( 277) hydrogen bonds : angle 4.05973 ( 810) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.49969 ( 2) covalent geometry : bond 0.00312 ( 4152) covalent geometry : angle 0.57273 ( 5661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.421 Fit side-chains REVERT: B 19 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6968 (ttm-80) REVERT: A 278 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7168 (tt) REVERT: A 459 TYR cc_start: 0.3287 (OUTLIER) cc_final: 0.2556 (m-10) outliers start: 17 outliers final: 9 residues processed: 83 average time/residue: 0.9892 time to fit residues: 85.3938 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141381 restraints weight = 4906.835| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.22 r_work: 0.3479 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4154 Z= 0.154 Angle : 0.592 9.074 5666 Z= 0.309 Chirality : 0.041 0.150 645 Planarity : 0.004 0.024 690 Dihedral : 4.517 19.616 582 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.76 % Allowed : 17.84 % Favored : 78.40 % 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: 2.18 (0.37), residues: 501 helix: 2.17 (0.29), residues: 300 sheet: 0.41 (0.57), residues: 59 loop : 0.44 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.001 0.000 HIS A 200 PHE 0.012 0.002 PHE A 439 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 0.83495 ( 3) hydrogen bonds : bond 0.04496 ( 277) hydrogen bonds : angle 4.10662 ( 810) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.54122 ( 2) covalent geometry : bond 0.00358 ( 4152) covalent geometry : angle 0.59173 ( 5661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.404 Fit side-chains REVERT: B 19 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6981 (ttm-80) REVERT: A 278 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7194 (tt) REVERT: A 459 TYR cc_start: 0.3959 (OUTLIER) cc_final: 0.3129 (m-10) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 1.1709 time to fit residues: 99.5505 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 37 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.141807 restraints weight = 4879.277| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.38 r_work: 0.3426 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4154 Z= 0.144 Angle : 0.578 9.358 5666 Z= 0.301 Chirality : 0.041 0.148 645 Planarity : 0.004 0.025 690 Dihedral : 4.446 19.352 582 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.52 % Allowed : 18.08 % Favored : 78.40 % 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: 2.23 (0.37), residues: 501 helix: 2.22 (0.29), residues: 300 sheet: 0.48 (0.57), residues: 59 loop : 0.40 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.031 0.002 PHE A 279 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 0.85258 ( 3) hydrogen bonds : bond 0.04374 ( 277) hydrogen bonds : angle 4.07125 ( 810) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.52269 ( 2) covalent geometry : bond 0.00330 ( 4152) covalent geometry : angle 0.57756 ( 5661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.341 Fit side-chains REVERT: B 19 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6999 (ttm-80) REVERT: A 459 TYR cc_start: 0.3912 (OUTLIER) cc_final: 0.3121 (m-10) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 1.4351 time to fit residues: 120.7574 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.145994 restraints weight = 4800.530| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.21 r_work: 0.3432 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4154 Z= 0.165 Angle : 0.607 9.308 5666 Z= 0.314 Chirality : 0.042 0.151 645 Planarity : 0.004 0.024 690 Dihedral : 4.557 19.477 582 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.05 % Allowed : 19.01 % Favored : 77.93 % 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: 2.14 (0.37), residues: 501 helix: 2.14 (0.29), residues: 300 sheet: 0.43 (0.57), residues: 59 loop : 0.41 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.013 0.002 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 0.90074 ( 3) hydrogen bonds : bond 0.04608 ( 277) hydrogen bonds : angle 4.15533 ( 810) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.53987 ( 2) covalent geometry : bond 0.00385 ( 4152) covalent geometry : angle 0.60676 ( 5661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.47 seconds wall clock time: 77 minutes 56.79 seconds (4676.79 seconds total)