Starting phenix.real_space_refine on Wed Jul 1 21:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2026/7e23_30950.map" } resolution = 3.3 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= 0.053 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 13 5.16 5 C 2001 2.51 5 N 519 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3133 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 756 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 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 chiralities: 1 Time building chain proxies: 0.83, per 1000 atoms: 0.26 Number of scatterers: 3133 At special positions: 0 Unit cell: (60.48, 74.52, 99.36, 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 13 16.00 O 600 8.00 N 519 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 73.5 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.628A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.614A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.574A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.541A pdb=" N ASN B 58 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TRP B 34 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.528A pdb=" N ALA B 91 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.951A pdb=" N LEU C 73 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.593A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 141 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: 0.37 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 985 1.34 - 1.46: 836 1.46 - 1.58: 1379 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3214 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" CB ARG B 66 " pdb=" CG ARG B 66 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" C SER B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.92e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 1.458 1.442 0.016 1.40e-02 5.10e+03 1.27e+00 ... (remaining 3209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 4236 2.00 - 4.00: 120 4.00 - 6.00: 12 6.00 - 8.01: 6 8.01 - 10.01: 3 Bond angle restraints: 4377 Sorted by residual: angle pdb=" N ARG C 61 " pdb=" CA ARG C 61 " pdb=" C ARG C 61 " ideal model delta sigma weight residual 114.75 108.44 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 112.00 101.99 10.01 2.20e+00 2.07e-01 2.07e+01 angle pdb=" C SER C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN C 93 " pdb=" N TRP C 94 " pdb=" CA TRP C 94 " ideal model delta sigma weight residual 121.80 113.47 8.33 2.44e+00 1.68e-01 1.17e+01 ... (remaining 4372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1682 17.73 - 35.46: 159 35.46 - 53.19: 23 53.19 - 70.92: 5 70.92 - 88.64: 4 Dihedral angle restraints: 1873 sinusoidal: 712 harmonic: 1161 Sorted by residual: dihedral pdb=" CA PHE C 71 " pdb=" C PHE C 71 " pdb=" N THR C 72 " pdb=" CA THR C 72 " ideal model delta harmonic sigma weight residual 180.00 137.99 42.01 0 5.00e+00 4.00e-02 7.06e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA THR C 69 " pdb=" C THR C 69 " pdb=" N ASP C 70 " pdb=" CA ASP C 70 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 301 0.039 - 0.078: 124 0.078 - 0.117: 35 0.117 - 0.156: 16 0.156 - 0.195: 3 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA PHE C 71 " pdb=" N PHE C 71 " pdb=" C PHE C 71 " pdb=" CB PHE C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 476 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 60 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 61 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 71 " -0.022 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE C 71 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 71 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " 0.008 2.00e-02 2.50e+03 1.22e-02 3.74e+00 pdb=" CG TRP B 47 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 2966 3.23 - 3.79: 4598 3.79 - 4.34: 6234 4.34 - 4.90: 10604 Nonbonded interactions: 24484 Sorted by model distance: nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.123 3.040 nonbonded pdb=" O SER C 63 " pdb=" OG SER C 77 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 22 " model vdw 2.220 3.040 nonbonded pdb=" O LYS A 417 " pdb=" ND2 ASN A 422 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 28 " pdb=" O HIS B 53 " model vdw 2.246 3.040 ... (remaining 24479 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: 2.300 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.660 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 3220 Z= 0.196 Angle : 0.827 10.007 4390 Z= 0.456 Chirality : 0.051 0.195 479 Planarity : 0.006 0.059 561 Dihedral : 14.447 88.644 1122 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.70 (0.41), residues: 393 helix: -5.03 (0.42), residues: 20 sheet: -2.14 (0.45), residues: 125 loop : -2.50 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.017 0.002 TYR C 49 PHE 0.036 0.002 PHE C 71 TRP 0.031 0.002 TRP B 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 3214) covalent geometry : angle 0.82520 / 0.46 ( 4377) SS BOND : bond 0.00134 / 0.06 ( 5) SS BOND : angle 1.22991 / 0.79 ( 10) hydrogen bonds : bond 0.17827 / 9.16 ( 61) hydrogen bonds : angle 8.42416 / 5.50 ( 141) link_NAG-ASN : bond 0.00091 / 0.05 ( 1) link_NAG-ASN : angle 1.20822 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0483 time to fit residues: 3.3692 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138159 restraints weight = 4731.746| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.65 r_work: 0.3707 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3220 Z= 0.143 Angle : 0.736 8.077 4390 Z= 0.376 Chirality : 0.048 0.193 479 Planarity : 0.007 0.114 561 Dihedral : 6.487 41.974 442 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 1.78 % Allowed : 11.24 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.59 (0.41), residues: 393 helix: -5.00 (0.44), residues: 20 sheet: -1.86 (0.45), residues: 125 loop : -2.54 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.031 0.001 PHE C 71 TRP 0.011 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3214) covalent geometry : angle 0.73389 / 0.38 ( 4377) SS BOND : bond 0.00227 / 0.12 ( 5) SS BOND : angle 1.26763 / 0.80 ( 10) hydrogen bonds : bond 0.03658 / 2.12 ( 61) hydrogen bonds : angle 6.99194 / 4.54 ( 141) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.28568 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.116 Fit side-chains REVERT: C 36 TYR cc_start: 0.7346 (m-80) cc_final: 0.6774 (m-80) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.0677 time to fit residues: 4.4121 Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136652 restraints weight = 4692.208| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.66 r_work: 0.3692 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3220 Z= 0.169 Angle : 0.734 9.291 4390 Z= 0.372 Chirality : 0.048 0.192 479 Planarity : 0.007 0.109 561 Dihedral : 6.446 41.898 442 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 2.37 % Allowed : 13.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.60 (0.41), residues: 393 helix: -4.90 (0.41), residues: 26 sheet: -1.79 (0.45), residues: 126 loop : -2.53 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 66 TYR 0.014 0.002 TYR C 49 PHE 0.034 0.002 PHE C 71 TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 3214) covalent geometry : angle 0.73260 / 0.37 ( 4377) SS BOND : bond 0.00223 / 0.11 ( 5) SS BOND : angle 1.14673 / 0.69 ( 10) hydrogen bonds : bond 0.03609 / 2.10 ( 61) hydrogen bonds : angle 6.57060 / 4.35 ( 141) link_NAG-ASN : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : angle 1.30701 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.120 Fit side-chains REVERT: A 457 ARG cc_start: 0.8710 (ttt-90) cc_final: 0.8221 (ttt-90) REVERT: B 47 TRP cc_start: 0.6213 (OUTLIER) cc_final: 0.5643 (t60) REVERT: C 36 TYR cc_start: 0.7503 (m-80) cc_final: 0.6424 (m-80) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.0739 time to fit residues: 4.7111 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137487 restraints weight = 4667.924| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.61 r_work: 0.3688 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3220 Z= 0.154 Angle : 0.717 10.010 4390 Z= 0.362 Chirality : 0.047 0.192 479 Planarity : 0.007 0.103 561 Dihedral : 6.269 41.447 442 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 3.55 % Allowed : 15.68 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.55 (0.41), residues: 393 helix: -4.91 (0.40), residues: 26 sheet: -1.73 (0.45), residues: 126 loop : -2.49 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.033 0.002 PHE C 71 TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 3214) covalent geometry : angle 0.71611 / 0.36 ( 4377) SS BOND : bond 0.00219 / 0.12 ( 5) SS BOND : angle 0.94993 / 0.54 ( 10) hydrogen bonds : bond 0.03334 / 1.96 ( 61) hydrogen bonds : angle 6.53867 / 4.33 ( 141) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 1.21666 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.069 Fit side-chains REVERT: A 334 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6855 (t0) REVERT: A 457 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.8114 (ttt-90) REVERT: B 47 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5562 (t60) REVERT: C 36 TYR cc_start: 0.7583 (m-80) cc_final: 0.6595 (m-80) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.0603 time to fit residues: 4.0849 Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128944 restraints weight = 4752.774| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.93 r_work: 0.3554 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3220 Z= 0.135 Angle : 0.694 10.703 4390 Z= 0.350 Chirality : 0.046 0.183 479 Planarity : 0.006 0.093 561 Dihedral : 6.098 39.659 442 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 3.85 % Allowed : 18.64 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.49 (0.41), residues: 393 helix: -4.86 (0.43), residues: 26 sheet: -1.64 (0.45), residues: 126 loop : -2.48 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.014 0.001 TYR B 59 PHE 0.031 0.002 PHE C 71 TRP 0.011 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 3214) covalent geometry : angle 0.69198 / 0.35 ( 4377) SS BOND : bond 0.00115 / 0.06 ( 5) SS BOND : angle 1.26521 / 0.79 ( 10) hydrogen bonds : bond 0.03185 / 1.85 ( 61) hydrogen bonds : angle 6.51926 / 4.30 ( 141) link_NAG-ASN : bond 0.00137 / 0.07 ( 1) link_NAG-ASN : angle 1.16955 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8302 (pt0) cc_final: 0.8057 (pt0) REVERT: B 47 TRP cc_start: 0.6068 (OUTLIER) cc_final: 0.5533 (t60) REVERT: B 48 ILE cc_start: 0.8575 (pt) cc_final: 0.8159 (pt) REVERT: C 36 TYR cc_start: 0.7532 (m-80) cc_final: 0.6592 (m-80) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.0725 time to fit residues: 4.7630 Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130662 restraints weight = 4712.784| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.91 r_work: 0.3576 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3220 Z= 0.127 Angle : 0.690 11.205 4390 Z= 0.346 Chirality : 0.046 0.183 479 Planarity : 0.006 0.084 561 Dihedral : 5.935 38.872 442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 4.44 % Allowed : 18.34 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.38 (0.41), residues: 393 helix: -4.85 (0.45), residues: 26 sheet: -1.50 (0.46), residues: 126 loop : -2.44 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.029 0.001 PHE C 71 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3214) covalent geometry : angle 0.68737 / 0.35 ( 4377) SS BOND : bond 0.00173 / 0.08 ( 5) SS BOND : angle 1.33828 / 0.81 ( 10) hydrogen bonds : bond 0.03097 / 1.84 ( 61) hydrogen bonds : angle 6.45493 / 4.27 ( 141) link_NAG-ASN : bond 0.00151 / 0.08 ( 1) link_NAG-ASN : angle 1.13750 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.079 Fit side-chains REVERT: A 457 ARG cc_start: 0.8713 (ttt-90) cc_final: 0.8104 (ttt-90) REVERT: B 39 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 48 ILE cc_start: 0.8584 (pt) cc_final: 0.8342 (pt) REVERT: C 36 TYR cc_start: 0.7437 (m-80) cc_final: 0.6579 (m-80) outliers start: 15 outliers final: 10 residues processed: 59 average time/residue: 0.0466 time to fit residues: 3.3267 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127519 restraints weight = 4818.780| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.96 r_work: 0.3545 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3220 Z= 0.169 Angle : 0.752 11.235 4390 Z= 0.378 Chirality : 0.049 0.202 479 Planarity : 0.006 0.088 561 Dihedral : 6.138 38.153 442 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 3.85 % Allowed : 20.41 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.31 (0.41), residues: 393 helix: -4.91 (0.41), residues: 26 sheet: -1.41 (0.48), residues: 116 loop : -2.39 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.038 0.002 PHE C 71 TRP 0.009 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 3214) covalent geometry : angle 0.74498 / 0.37 ( 4377) SS BOND : bond 0.00497 / 0.21 ( 5) SS BOND : angle 2.27085 / 1.18 ( 10) hydrogen bonds : bond 0.03419 / 2.01 ( 61) hydrogen bonds : angle 6.43315 / 4.25 ( 141) link_NAG-ASN : bond 0.00124 / 0.07 ( 1) link_NAG-ASN : angle 1.27658 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.071 Fit side-chains REVERT: A 516 GLU cc_start: 0.8262 (pt0) cc_final: 0.7981 (pt0) REVERT: B 39 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 48 ILE cc_start: 0.8601 (pt) cc_final: 0.8380 (pt) REVERT: C 36 TYR cc_start: 0.7520 (m-80) cc_final: 0.6601 (m-80) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.0452 time to fit residues: 3.1444 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.154411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141352 restraints weight = 4892.067| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.72 r_work: 0.3725 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3220 Z= 0.133 Angle : 0.733 11.820 4390 Z= 0.367 Chirality : 0.048 0.183 479 Planarity : 0.006 0.081 561 Dihedral : 5.974 37.608 442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 3.55 % Allowed : 21.01 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.31 (0.41), residues: 393 helix: -4.85 (0.44), residues: 26 sheet: -1.45 (0.45), residues: 126 loop : -2.39 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.030 0.002 PHE C 71 TRP 0.012 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 3214) covalent geometry : angle 0.72629 / 0.36 ( 4377) SS BOND : bond 0.00753 / 0.29 ( 5) SS BOND : angle 2.18913 / 1.05 ( 10) hydrogen bonds : bond 0.03350 / 2.05 ( 61) hydrogen bonds : angle 6.34509 / 4.23 ( 141) link_NAG-ASN : bond 0.00132 / 0.07 ( 1) link_NAG-ASN : angle 1.12062 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.120 Fit side-chains REVERT: A 516 GLU cc_start: 0.8111 (pt0) cc_final: 0.7892 (pt0) REVERT: B 39 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: C 5 THR cc_start: 0.8255 (m) cc_final: 0.7746 (p) REVERT: C 36 TYR cc_start: 0.7492 (m-80) cc_final: 0.6643 (m-80) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.0491 time to fit residues: 3.3884 Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129802 restraints weight = 4853.031| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.97 r_work: 0.3569 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3220 Z= 0.146 Angle : 0.726 11.436 4390 Z= 0.366 Chirality : 0.048 0.187 479 Planarity : 0.006 0.083 561 Dihedral : 6.011 37.476 442 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Rotamer: Outliers : 3.55 % Allowed : 22.19 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.29 (0.41), residues: 393 helix: -4.86 (0.43), residues: 26 sheet: -1.42 (0.46), residues: 126 loop : -2.39 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.033 0.002 PHE C 71 TRP 0.010 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3214) covalent geometry : angle 0.71993 / 0.36 ( 4377) SS BOND : bond 0.00673 / 0.26 ( 5) SS BOND : angle 2.04807 / 0.96 ( 10) hydrogen bonds : bond 0.03376 / 2.04 ( 61) hydrogen bonds : angle 6.37196 / 4.21 ( 141) link_NAG-ASN : bond 0.00133 / 0.07 ( 1) link_NAG-ASN : angle 1.19288 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.070 Fit side-chains REVERT: A 516 GLU cc_start: 0.8310 (pt0) cc_final: 0.8046 (pt0) REVERT: B 39 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: C 5 THR cc_start: 0.8221 (m) cc_final: 0.7702 (p) REVERT: C 36 TYR cc_start: 0.7487 (m-80) cc_final: 0.6580 (m-80) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.0534 time to fit residues: 3.7648 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.0030 chunk 19 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.155769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142645 restraints weight = 4775.048| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.79 r_work: 0.3740 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3220 Z= 0.126 Angle : 0.701 12.271 4390 Z= 0.352 Chirality : 0.047 0.179 479 Planarity : 0.006 0.072 561 Dihedral : 5.845 36.145 442 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.99 % Favored : 86.01 % Rotamer: Outliers : 2.37 % Allowed : 22.78 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.02 (0.42), residues: 393 helix: -5.11 (0.33), residues: 18 sheet: -1.33 (0.46), residues: 126 loop : -2.22 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.012 0.001 TYR C 49 PHE 0.031 0.001 PHE C 71 TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3214) covalent geometry : angle 0.69630 / 0.35 ( 4377) SS BOND : bond 0.00572 / 0.24 ( 5) SS BOND : angle 1.73786 / 0.86 ( 10) hydrogen bonds : bond 0.03248 / 1.98 ( 61) hydrogen bonds : angle 6.29379 / 4.20 ( 141) link_NAG-ASN : bond 0.00134 / 0.07 ( 1) link_NAG-ASN : angle 1.06411 / 0.61 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.079 Fit side-chains REVERT: A 369 TYR cc_start: 0.7138 (t80) cc_final: 0.6893 (t80) REVERT: A 444 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7050 (mtmm) REVERT: A 516 GLU cc_start: 0.8134 (pt0) cc_final: 0.7907 (pt0) REVERT: B 39 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 5 THR cc_start: 0.8235 (m) cc_final: 0.7799 (p) REVERT: C 36 TYR cc_start: 0.7447 (m-80) cc_final: 0.6594 (m-80) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.0598 time to fit residues: 3.8320 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137492 restraints weight = 4770.588| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.75 r_work: 0.3695 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3220 Z= 0.164 Angle : 0.732 11.661 4390 Z= 0.369 Chirality : 0.049 0.193 479 Planarity : 0.006 0.084 561 Dihedral : 6.102 36.592 442 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 2.37 % Allowed : 23.67 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -3.16 (0.41), residues: 393 helix: -4.95 (0.38), residues: 26 sheet: -1.31 (0.48), residues: 116 loop : -2.26 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.037 0.002 PHE C 71 TRP 0.009 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 3214) covalent geometry : angle 0.72639 / 0.37 ( 4377) SS BOND : bond 0.00635 / 0.26 ( 5) SS BOND : angle 1.88655 / 0.91 ( 10) hydrogen bonds : bond 0.03527 / 2.11 ( 61) hydrogen bonds : angle 6.34216 / 4.20 ( 141) link_NAG-ASN : bond 0.00137 / 0.07 ( 1) link_NAG-ASN : angle 1.28940 / 0.73 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.34 seconds wall clock time: 16 minutes 9.36 seconds (969.36 seconds total)