Starting phenix.real_space_refine on Wed Sep 17 04:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g5k_51088/09_2025/9g5k_51088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g5k_51088/09_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_51088/09_2025/9g5k_51088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g5k_51088/09_2025/9g5k_51088.map" model { file = "/net/cci-nas-00/data/ceres_data/9g5k_51088/09_2025/9g5k_51088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g5k_51088/09_2025/9g5k_51088.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.22, per 1000 atoms: 0.30 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: 0.38 Conformation dependent library (CDL) restraints added in 171.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.71 Time building geometry restraints manager: 0.51 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: 5.360 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.370 Find NCS groups from input model: 0.010 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:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 78 TYR 0.011 0.001 TYR A 280 PHE 0.008 0.001 PHE A 279 TRP 0.022 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4152) covalent geometry : angle 0.60497 ( 5661) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.18964 ( 2) hydrogen bonds : bond 0.17004 ( 277) hydrogen bonds : angle 6.76142 ( 810) link_NAG-ASN : bond 0.02143 ( 1) link_NAG-ASN : angle 4.99903 ( 3) *********************** 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 : 0.162 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: 0.5912 time to fit residues: 49.4485 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 : 0.160 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144841 restraints weight = 5004.452| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.23 r_work: 0.3412 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4154 Z= 0.226 Angle : 0.675 9.496 5666 Z= 0.351 Chirality : 0.045 0.167 645 Planarity : 0.005 0.036 690 Dihedral : 5.701 57.678 587 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.93 % Allowed : 14.55 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.37), residues: 501 helix: 1.91 (0.29), residues: 298 sheet: -0.27 (0.59), residues: 59 loop : 0.23 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.021 0.002 TYR B 113 PHE 0.015 0.002 PHE A 439 TRP 0.024 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4152) covalent geometry : angle 0.67515 ( 5661) SS BOND : bond 0.00434 ( 1) SS BOND : angle 0.70156 ( 2) hydrogen bonds : bond 0.05708 ( 277) hydrogen bonds : angle 4.66499 ( 810) link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 1.11065 ( 3) *********************** 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 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.158 Fit side-chains REVERT: B 19 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7200 (tmm-80) REVERT: B 89 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 78 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.5941 (mpt-90) REVERT: A 278 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7173 (tt) REVERT: A 349 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7116 (tp) outliers start: 21 outliers final: 6 residues processed: 87 average time/residue: 0.5395 time to fit residues: 48.5429 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 278 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 435 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141603 restraints weight = 4908.728| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.31 r_work: 0.3443 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4154 Z= 0.155 Angle : 0.574 8.116 5666 Z= 0.303 Chirality : 0.041 0.149 645 Planarity : 0.004 0.033 690 Dihedral : 5.442 55.222 585 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.23 % Allowed : 16.43 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.37), residues: 501 helix: 2.11 (0.29), residues: 301 sheet: -0.02 (0.58), residues: 59 loop : 0.27 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 402 TYR 0.015 0.002 TYR A 280 PHE 0.012 0.002 PHE A 439 TRP 0.022 0.002 TRP A 94 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4152) covalent geometry : angle 0.57399 ( 5661) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.56058 ( 2) hydrogen bonds : bond 0.04853 ( 277) hydrogen bonds : angle 4.30649 ( 810) link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 0.88190 ( 3) *********************** 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 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.164 Fit side-chains REVERT: A 278 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 440 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (tp) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 0.5163 time to fit residues: 46.5249 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU 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 164 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.155575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140879 restraints weight = 4933.605| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.18 r_work: 0.3425 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4154 Z= 0.171 Angle : 0.593 7.948 5666 Z= 0.312 Chirality : 0.043 0.153 645 Planarity : 0.004 0.030 690 Dihedral : 4.686 22.251 582 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.69 % Allowed : 16.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.37), residues: 501 helix: 2.07 (0.29), residues: 300 sheet: 0.10 (0.58), residues: 59 loop : 0.32 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 402 TYR 0.018 0.002 TYR A 280 PHE 0.015 0.002 PHE A 279 TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4152) covalent geometry : angle 0.59293 ( 5661) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.53017 ( 2) hydrogen bonds : bond 0.04915 ( 277) hydrogen bonds : angle 4.28154 ( 810) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 0.99959 ( 3) *********************** 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 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.153 Fit side-chains REVERT: B 89 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 166 ASN cc_start: 0.8440 (t0) cc_final: 0.8212 (t0) REVERT: A 278 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7231 (tt) REVERT: A 440 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8238 (tp) outliers start: 20 outliers final: 10 residues processed: 89 average time/residue: 0.4930 time to fit residues: 45.3932 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU 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 164 LEU 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 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.155707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139540 restraints weight = 4970.945| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.26 r_work: 0.3419 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4154 Z= 0.207 Angle : 0.635 8.986 5666 Z= 0.332 Chirality : 0.044 0.156 645 Planarity : 0.004 0.029 690 Dihedral : 5.062 29.095 582 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.16 % Allowed : 16.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 501 helix: 1.92 (0.29), residues: 300 sheet: 0.09 (0.59), residues: 59 loop : 0.35 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 78 TYR 0.018 0.002 TYR A 280 PHE 0.015 0.002 PHE A 439 TRP 0.022 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4152) covalent geometry : angle 0.63453 ( 5661) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.46738 ( 2) hydrogen bonds : bond 0.05226 ( 277) hydrogen bonds : angle 4.37203 ( 810) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 0.96432 ( 3) *********************** 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: 22 poor density : 74 time to evaluate : 0.150 Fit side-chains REVERT: B 89 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 166 ASN cc_start: 0.8424 (t0) cc_final: 0.8181 (t0) REVERT: A 278 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7302 (tt) REVERT: A 459 TYR cc_start: 0.3778 (OUTLIER) cc_final: 0.3060 (m-10) outliers start: 22 outliers final: 10 residues processed: 87 average time/residue: 0.5060 time to fit residues: 45.5551 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU 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 164 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.157258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.141176 restraints weight = 5021.020| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.26 r_work: 0.3428 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2004 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= 0.163 Angle : 0.593 9.292 5666 Z= 0.309 Chirality : 0.042 0.151 645 Planarity : 0.004 0.029 690 Dihedral : 4.834 29.588 582 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.99 % Allowed : 17.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.37), residues: 501 helix: 2.02 (0.29), residues: 300 sheet: 0.25 (0.59), residues: 59 loop : 0.38 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.019 0.002 TYR A 280 PHE 0.018 0.002 PHE A 279 TRP 0.022 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4152) covalent geometry : angle 0.59273 ( 5661) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.55932 ( 2) hydrogen bonds : bond 0.04749 ( 277) hydrogen bonds : angle 4.23980 ( 810) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 0.93079 ( 3) *********************** 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: 17 poor density : 76 time to evaluate : 0.114 Fit side-chains REVERT: B 19 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7044 (tmm-80) REVERT: B 89 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 166 ASN cc_start: 0.8409 (t0) cc_final: 0.8164 (t0) REVERT: A 278 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7217 (tt) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.5052 time to fit residues: 44.4435 Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 164 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.158056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.141774 restraints weight = 4994.001| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.28 r_work: 0.3452 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4154 Z= 0.151 Angle : 0.578 9.120 5666 Z= 0.301 Chirality : 0.041 0.150 645 Planarity : 0.004 0.028 690 Dihedral : 4.688 27.002 582 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.93 % Allowed : 16.90 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.37), residues: 501 helix: 2.09 (0.29), residues: 300 sheet: 0.36 (0.59), residues: 59 loop : 0.39 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.019 0.002 TYR A 280 PHE 0.012 0.001 PHE A 439 TRP 0.021 0.002 TRP A 94 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4152) covalent geometry : angle 0.57801 ( 5661) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.51469 ( 2) hydrogen bonds : bond 0.04559 ( 277) hydrogen bonds : angle 4.15741 ( 810) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 0.93319 ( 3) *********************** 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 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.115 Fit side-chains REVERT: B 19 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7007 (tmm-80) REVERT: B 89 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 166 ASN cc_start: 0.8414 (t0) cc_final: 0.8176 (t0) REVERT: A 278 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7204 (tt) REVERT: A 459 TYR cc_start: 0.3898 (OUTLIER) cc_final: 0.3131 (m-10) outliers start: 21 outliers final: 12 residues processed: 89 average time/residue: 0.4607 time to fit residues: 42.5695 Evaluate side-chains 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 79 VAL 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 132 SER Chi-restraints excluded: chain A residue 164 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.140002 restraints weight = 4861.580| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.36 r_work: 0.3415 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2092 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= 0.170 Angle : 0.601 9.484 5666 Z= 0.312 Chirality : 0.042 0.153 645 Planarity : 0.004 0.028 690 Dihedral : 4.728 26.272 582 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.69 % Allowed : 18.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.37), residues: 501 helix: 2.04 (0.29), residues: 300 sheet: 0.34 (0.59), residues: 59 loop : 0.36 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.019 0.002 TYR A 280 PHE 0.023 0.002 PHE A 279 TRP 0.020 0.002 TRP A 94 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4152) covalent geometry : angle 0.60032 ( 5661) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.50820 ( 2) hydrogen bonds : bond 0.04774 ( 277) hydrogen bonds : angle 4.19978 ( 810) link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 0.93841 ( 3) *********************** 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 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.164 Fit side-chains REVERT: B 19 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7057 (tmm-80) REVERT: B 89 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 166 ASN cc_start: 0.8458 (t0) cc_final: 0.8213 (t0) REVERT: A 278 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7193 (tt) REVERT: A 459 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.3086 (m-10) outliers start: 20 outliers final: 12 residues processed: 85 average time/residue: 0.4841 time to fit residues: 42.7010 Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 79 VAL 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 132 SER Chi-restraints excluded: chain A residue 164 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140890 restraints weight = 4998.123| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.32 r_work: 0.3410 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4154 Z= 0.187 Angle : 0.624 9.700 5666 Z= 0.324 Chirality : 0.043 0.154 645 Planarity : 0.004 0.028 690 Dihedral : 4.846 28.372 582 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.93 % Allowed : 18.31 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.37), residues: 501 helix: 1.96 (0.29), residues: 300 sheet: 0.27 (0.59), residues: 59 loop : 0.34 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 402 TYR 0.019 0.002 TYR A 280 PHE 0.014 0.002 PHE A 439 TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4152) covalent geometry : angle 0.62385 ( 5661) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.49648 ( 2) hydrogen bonds : bond 0.04939 ( 277) hydrogen bonds : angle 4.25355 ( 810) link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 0.91762 ( 3) *********************** 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 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.152 Fit side-chains REVERT: B 19 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7073 (tmm-80) REVERT: B 89 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 115 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8429 (ttm) REVERT: A 134 GLU cc_start: 0.8216 (pt0) cc_final: 0.7941 (pt0) REVERT: A 166 ASN cc_start: 0.8456 (t0) cc_final: 0.8209 (t0) REVERT: A 278 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7235 (tt) REVERT: A 459 TYR cc_start: 0.3952 (OUTLIER) cc_final: 0.3305 (m-10) outliers start: 21 outliers final: 12 residues processed: 82 average time/residue: 0.4882 time to fit residues: 41.5601 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 79 VAL 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 115 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 LEU 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 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 200 HIS A 297 ASN A 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143847 restraints weight = 4852.337| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.35 r_work: 0.3458 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4154 Z= 0.122 Angle : 0.554 9.492 5666 Z= 0.287 Chirality : 0.039 0.143 645 Planarity : 0.004 0.027 690 Dihedral : 4.273 20.889 582 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.46 % Allowed : 18.31 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.37), residues: 501 helix: 2.25 (0.29), residues: 300 sheet: 0.46 (0.56), residues: 57 loop : 0.40 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.020 0.001 TYR A 280 PHE 0.030 0.001 PHE A 279 TRP 0.023 0.001 TRP A 94 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4152) covalent geometry : angle 0.55377 ( 5661) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.51144 ( 2) hydrogen bonds : bond 0.04081 ( 277) hydrogen bonds : angle 3.99145 ( 810) link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 0.86662 ( 3) ********************** 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 102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.105 Fit side-chains REVERT: B 19 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7003 (tmm-80) REVERT: A 115 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: A 134 GLU cc_start: 0.8108 (pt0) cc_final: 0.7828 (pt0) REVERT: A 166 ASN cc_start: 0.8372 (t0) cc_final: 0.8118 (t0) REVERT: A 459 TYR cc_start: 0.3707 (OUTLIER) cc_final: 0.3202 (m-10) outliers start: 19 outliers final: 6 residues processed: 92 average time/residue: 0.4707 time to fit residues: 44.8807 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 SER 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 9 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143749 restraints weight = 4929.929| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.14 r_work: 0.3447 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2342 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= 0.153 Angle : 0.603 9.530 5666 Z= 0.311 Chirality : 0.042 0.151 645 Planarity : 0.004 0.028 690 Dihedral : 4.410 19.613 582 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.82 % Allowed : 19.48 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.37), residues: 501 helix: 2.18 (0.29), residues: 299 sheet: 0.35 (0.56), residues: 57 loop : 0.37 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.020 0.002 TYR A 280 PHE 0.012 0.002 PHE A 439 TRP 0.023 0.002 TRP A 94 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4152) covalent geometry : angle 0.60312 ( 5661) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.48832 ( 2) hydrogen bonds : bond 0.04475 ( 277) hydrogen bonds : angle 4.10856 ( 810) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 0.81863 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.89 seconds wall clock time: 29 minutes 36.68 seconds (1776.68 seconds total)